The Journey Begins with your microbiome

Thanks for joining me!

This is a companion site to the analysis site at: https://microbiomeprescription.com/

The intent of this site to assist people with health issues that are, or could be, microbiome connected. There are MANY conditions known to have the severity being a function of the microbiome dysfunction, including Autism, Alzheimer’s, Anxiety and Depression. See this list of studies from the US National Library of Medicine. Individual symptoms like brain fog, anxiety and depression have strong statistical association to the microbiome. A few of them are listed here.

The base rule of the site is to avoid speculation, keep to facts from published studies and to facts from statistical analysis(with the source data available for those wish to replicate the results). Internet hearsay is avoid like the plague it is.

The Microbiome as a Key to Health

Continue reading “The Journey Begins with your microbiome”

Converting GI-Map to Percentage

First, some fundamentals:

Units of Measure

The notation “3.3e12” is scientific notation, which is a compact way of representing very large numbers. In this notation, the “e” stands for “exponent.” So, “3.3e12” means 3.3×10^12 .

Breaking it down:

  • 3.3 is the coefficient or mantissa.
  • 10 is the base.
  • 12 is the exponent or power of 10.

Therefore, “3.3e12” is equivalent to 3.3 multiplied by 10 raised to the power of 12 , which equals 3.3 followed by 12 zeros:

3.3×1012=3,300,000,000,000.

In other words, “3.3e12” represents 3.3 trillion.

Total Bacteria

Ideally, you would add up all of the phylums; unfortunately GI-MAP only provides two

So the total in this sample is 7.15e12 which is above the reference range max of 3.6e12. So for the purposes of this discussion, we will assume 7.15e12 (with the difference from reference being other phylums).

How does GI-MAP work?

The GI-MAP (Gastrointestinal Microbial Assay Plus) is a diagnostic tool used to assess the composition of bacteria, parasites, and other microorganisms present in the gastrointestinal tract. It utilizes a technique called quantitative polymerase chain reaction (qPCR) to measure the abundance of specific microbial DNA in a stool sample. Here’s how it works:

  1. Stool Sample Collection: A patient provides a stool sample, typically collected at home and sent to a laboratory for analysis.
  2. DNA Extraction: The laboratory extracts microbial DNA from the stool sample. This step involves breaking open the cells of the microorganisms to release their genetic material.
  3. Primer Design: Primers are short DNA sequences designed to bind specifically to the target DNA sequences of interest. For the GI-MAP, these primers target specific regions of the microbial DNA that are unique to certain bacterial species, parasites, or other microorganisms.
  4. qPCR Amplification: The extracted microbial DNA is mixed with the primers and other reagents in a reaction mixture. The qPCR machine then cycles through a series of temperature changes to amplify (copy) the target DNA sequences. Each cycle doubles the amount of DNA present, allowing for the exponential amplification of the target DNA.
  5. Fluorescent Detection: During the qPCR process, fluorescent reporter molecules are incorporated into the DNA as it is amplified. As the amount of amplified DNA increases, so does the fluorescence signal. This allows the qPCR machine to detect and quantify the amount of DNA present in the sample.
  6. Data Analysis: The fluorescence data collected during the qPCR process are analyzed to determine the abundance of specific microbial DNA targets in the stool sample. By comparing the fluorescence signals to standard curves generated from known concentrations of DNA, the laboratory can quantify the relative abundance of different microorganisms present in the sample.

Converting to Percentage

Now, how do we convert. The easy way is to use EXCEL or other spreadsheets. Example of the formula is below.

Then change the display from Scientific to Percentage

We now have the percentages

That is it!

You can then compare to Jason Hawrelak Criteria for Healthy Gut or other criteria.

A word of Caution

One word of caution…   to illustrate, take GI-MAP reference ranges and convert to  Percentiles.

this becomes 0.0007 – 0.28% 

then go to https://microbiomeprescription.com/library/details?taxon=841

Their measurement scale seems inconsistent with other scales (16s and Shotgun)

Revisions to the Health Analysis Page

The calculations were audited and several errors found and corrected.

Significant changes

Charts against samples from the same lab are shown by clicking on the chart icon.

For example:

NOTE: negative numbers means bacteria are consuming, thus less consumption means more gets to the body. We calculate both producers and consumers.

Information on what something means

There is a red question mark that will show more information about the measure

A walkthrough video is below.

Walkthru of new and revised features on the Health Indicators Page (youtube.com)

Saving Money with Probiotics

Probiotics are a HUGH profit margin. The cost to produce is pretty constant. The difference per BCFU from the cheapest to the most expensive is 650x (i.e. 65,000% difference). You can cut your supplement costs greatly with some careful shopping around and computing the cost per BCFU.

Below are some buying options. I will use Lactobacillus reuteri  to illustrate the price issues

BioGaia Gastrus

30 x 0.2 BCFU = 6 BCFU for $30.00 or 0.2 BCFU per dollar

Super Smart

60 x 5 BCFU = 300 BFU for $20 or 15 BCFU per dollar

Toniiq

They appear to have only one single strain probiotic for sale.

50 BCFU x 60 = 3000 BCFU for $22. or 136 BCFU per dollar

Custom Probiotics

They use a researched strain (different from the above). They are probiotics ONLY, no filler.

50/.8 * 60 BCFU = 3650 BCFU for $100 = 36.5 BCFU per dollar

Maple Life Sciences

50 grams at 20 BCFU/gram = 1000 BFCU for $15.00 = 66 BCFU per dollar
They are probiotics with fructooligosaccharides only, no other fillers. Certified Organic

Shotgun vs 16s OR Biomesight vs Xenogene

As a reminder, Microbiome Prescription is a “best efforts” site. We do the best that we can with the data that is available.

Request from Reader

Hello Ken, 

I would kindly like to ask your opinion on this. I did three BiomeSight tests in three years, then one Xenogene. The Xenogene and last BiomeSight were 10 days apart. 

BiomeSight was telling me for three years that my butyrate producers were awesome and my F.Prau was great. Then Xenogene told me the exact opposite. BiomeSight results being so good for so long, I always assumed I have no problem in the microbiome so I kept my diet (15g of fiber at max, lots of meat, veggiest mainly potatoes – no 30-40 different veg/fruit per week). Butyrate producers and F.Prau this high on this diet is a little hard to believe, so I came to the conclusion that BiomeSight is completely off, at least for me. 

I remember the Taxonomic nightmare article you wrote and I understand that I cant directly compare two test providers. But when one test tells you that your microbiome is a rockstar and the other tells you its a zombie, its hard to see the usefulness of biomeSight testing. I kindof hope there is some magic that Im forgetting and the biomeSight tests will not prove to be a waste of time and money. 

The Xenogene values are percentages of bacteria only (i.e. # F. Prau / # total bacteria), so its “the same thing” as in biomeSight results. Just to be clear that its not # F.Prau / (# bacteria + # protozoa + # archaea + # fungi).

Explanation

Numbers always need to be interpreted against reference ranges.

Standard Lab Reference Ranges

If you go to the Akkermansia reference page, we see the following:

LabMeanStandard DeviationShift in S.D.
Xenogene0.693 %1.074 %– 0.9
Biomesight1.393 %4.111 %+.83

In other words, both test results were within 1 standard deviation of the mean – that will usually be interpreted as in the normal/reference range. The formula is easy:

(Your Value - Mean) / Standard Deviation

You can do this for each of the bacteria in your report. If the resulting value is between -1.6 and +1.6, you are clearly in the reference ranges.

Lab Provided Ranges

Xenogene provides ranges — this means that over 70% of xenogene files uploaded to MP are below the reference range.

Biomesight reference ranges are below

Every value is within the reference ranges. We have a disagreement.

Dr. Jason Hawrelak Recommendations

His ranges are 1-5% for Akkermansia. These are much less than Biomesight and bigger than xenogene.
User Feedback: “Dr. Hawrelak’s ranges – how can Dr. Hawrelak have a general range on some bacterium w/o stating which lab he uses for this? Considering all labs report different numbers due to the taxonomy nightmare, I don’t understand how there can be “one range to rule them all”

I agree totally, some labs cites him as an authority because they lack the skilled resources to determine their lab specific ranges, Often I have seen ranges from a published studied applied to numbers from a totally different processing pipeline – when challenged they cite “it’s an authority“. Some more readings:

As a FYI: I include his ranges because people have requested it. I provide choices and not judgements.

Microbiome Prescription Ranges

We do not have enough data to independently compute xenogene. Xenogene samples are part of “Other Labs”. The Kaltoft-Moldrup ranges are:

  • Other Labs: 0 – 7%
  • Biomesight: 0 -9.6%

Similarly using BoxPlot methodology,

  • Other Labs: 0 – 3.8%
  • Biomesight: 0 -1.7%

Note that Zero (0) is in range for many of these.

The Symptoms Factor

Identifying bacteria associated with symptoms depends on the number of samples uploaded with annotated symptoms. We do not have sufficient results with Xenogene, we do have sufficient for Biomesight with some 289 associations at present. Note this is pattern matching. “It has the ears of a German Shepard, it has a double coat of a German Shepard, it eyes color matches a German Shepard…etc. ” It may be German Shepard or it may be a Wolf or a Welsh Pembroke Corgi

For the latest Biomesight, we see a lot of matches to existing patterns

For Xenogene (which uses “Other Labs”) we have less and weaker matched

If you want to include your symptom in the suggestions report, biomesight is a better choice.

Eubiosis

Eubiosis is not very comparable, because Xenogene is mixed with all of the other odd labs. We have just 19 xenogene, not sufficient to do that much data, We have 61 samples from Thorne – same issue.

Follow up Questions

So my question was how can BiomeSight tell me my butyrate producers are 60% when its highly unlikely, just as with F.Prau being 19%. And the answers that I could imagine getting would be

  • you having 60% butyrate producers is the result of taxonomic hell, in some cases the positive measurement errors can add up resulting in a hugely overestimated sum – judging the SCFA producers in the biomeSight report is unreliable and should not be taken into consideration at all
  • OR the only relevant marker for abundance of SCFA producers is stool pH or SCFA measured in stool – use that instead of the SCFA producers % reported by ANY test provider
  • OR something else if the former two are nonsense

Butyrate evaluation is a good illustration minefield. Some observations:

  • Labs will usually qualify with “It is important to note that this is not a measure of these metabolites found in the stool sample.
  • One lab totals 9 Genus and 1 species.
  • Biomesight appears to total 21 genus
  • Another totals: 43 species
  • Microbiome Prescription is based on  KEGG: Kyoto Encyclopedia of Genes and Genomes :
    • 402 species that could produce butyrate
    • 515 species that could consume butyrate

MP is the only one that appears to include consumers (thus getting a net amount). The choice of genus and species is often based on the depth of research that each lab does. MP is based on the genetics of the bacteria as sequenced and aggregated by KEGG. We do not know if the genetics are activated or not (epigenetics).

What is missing are studies comparing various estimates from bacteria against actual directly determined levels of butyrate and other metabolites…

Second Issue: Percentage of WHAT?

Many labs pull a magical number out of the air, typically if you are over this number you are Satisfactory, below Not Satisfactory. MP gives a percentile ranking against others samples using the same lab. If you are over 30%ile, I would deem it to not need work — but that is a personal judgement call, the numbers are there for you.

Bottom Line

Microbiome reports are full of uncertainty aka fuzzy data. Fuzzy data is not a strong selling point for businesses. Claiming accuracy and correctness is a great marketing ploy. If there are no legal/financial consequences of these dubious claims then they will typically be made by some.

I have seen some labs that started by “just reporting the facts/numbers” and then drift into interpretations because marketing studies found that would increase business.

Xenogene (and Thorne) is good because of what else it reports that is not reported on Biomesight which may be part of your health issues. For items that seem very high, you should do some research on them and if any medical conditions are reported/associated with them.

On the other side, we have a lot of samples with annotated symptoms for Biomesight and Ombre. This means that suggestions to modify your microbiome (especially if symptoms are used) are likely better.

My usual advice is simple:

  • do one of Xenogene or Thorne to check for non bacteria issues (fungi, phages, etx)
  • use Biomesight or Ombre for regular testing and getting suggestions.

Psychoactive Probiotics! – 2024 Update for Glutamate

While Glutamate is not usually associated with being Psychoactive, it plays an important role

Excessive GABA may be associated with Huntington’s disease, epilepsy, and certain types of encephalopathies. Insufficient GABA may be associated with Anxiety Disorders, Epilepsy, Sleep Disorders, Mood Disorders, Substance Use Disorders, Movement Disorders, Neuropathic Pain and Autism Spectrum Disorders.

Excessive Dopamine may be associated with: Mania or Hypomania, Psychosis, Substance Use Disorders, Hyperactivity and Impulsivity, Tics and Tourette Syndrome, Sleep Disorders, Huntington’s Disease and Excessive Reward Seeking Behavior. Insufficient dopamine may be associated with: Parkinson’s Disease, Depression, Attention-Deficit/Hyperactivity Disorder (ADHD), Drug Addiction and Substance Use Disorders, Restless Legs Syndrome, Schizophrenia and Huntington’s Disease.

Excessive Glutamate may be associated with: Stroke, Traumatic Brain Injury (TBI), Neurodegenerative Diseases, Epilepsy, Migraine, Hypoxic-Ischemic Encephalopathy (HIE), Schizophrenia, Major Depressive Disorder, Bipolar Disorder and Trauma and Neuroinflammation. Insufficient Glutamate may be associated with Cognitive Impairment and Memory Disorders, Depression, Schizophrenia, Pain Disorders, Huntington’s Disease, Epilepsy, Neurodevelopmental Disorders and Sleep Disorders.

From Basolateral amygdala and stress-induced hyperexcitability affect motivated behaviors and addiction [2017]

Dietary Sources:

  • Protein-Rich Foods: Glutamate is naturally present in protein-containing foods. Foods high in protein, such as meat, poultry, fish, eggs, dairy products (especially aged cheeses), and legumes, contain significant amounts of glutamate.
  • Fermented Foods: Fermented foods contain glutamate due to the fermentation process, during which glutamate-producing bacteria break down proteins into amino acids. Examples include soy sauce, miso, tempeh, fermented vegetables (e.g., sauerkraut, kimchi), fermented dairy products (e.g., yogurt), and aged cheeses (e.g., Parmesan, Roquefort).
  • Seaweed: Certain types of seaweed, such as kombu (kelp), nori, and wakame, are rich sources of glutamate.
  • Tomatoes: Tomatoes and tomato-based products (e.g., tomato sauce, tomato paste) contain glutamate, contributing to their savory flavor.
  • Mushrooms: Some varieties of mushrooms, such as shiitake mushrooms, are naturally high in glutamate.

Producers

From Chat-GPT:

  • Lactobacillus species: Various species within the Lactobacillus genus are known to produce glutamate during fermentation. Examples include Lactobacillus brevis, Lactobacillus plantarum, and Lactobacillus fermentum. These bacteria are commonly used in the fermentation of foods such as sauerkraut, kimchi, pickles, and certain dairy products.
  • Bacillus subtilis: Bacillus subtilis is a Gram-positive bacterium known for its ability to produce glutamate. It is used in the fermentation of soybeans to produce traditional Japanese seasonings such as miso and soy sauce.
  • Corynebacterium glutamicum: This bacterium is widely used in industrial fermentation for the large-scale production of glutamate and glutamate-derived compounds. Corynebacterium glutamicum is a key organism in the production of monosodium glutamate (MSG), a food additive used to enhance flavor.
  • Streptococcus species: Some species of Streptococcus bacteria are capable of producing glutamate during fermentation. Streptococcus thermophilus, for example, is commonly used in the fermentation of yogurt and certain cheeses.
  • Propionibacterium freudenreichii: This bacterium is involved in the fermentation of Swiss cheese, where it produces various flavor compounds, including glutamate.

Psychoactive Probiotics! – 2024 Update for Dopamine

A reader asked me to do an update of my 2016 post Psychoactive Probiotics! There has been a lot of recent literature as shown on PubMed. Note that often these are strain specific and not generalized for species cited below. If you cannot find the strains specified in the studies, it may be worthwhile trying different brands of the species (with the most studied species being most probable).

Excessive Dopamine may be associated with: Mania or Hypomania, Psychosis, Substance Use Disorders, Hyperactivity and Impulsivity, Tics and Tourette Syndrome, Sleep Disorders, Huntington’s Disease and Excessive Reward Seeking Behavior. Insufficient dopamine may be associated with: Parkinson’s Disease, Depression, Attention-Deficit/Hyperactivity Disorder (ADHD), Drug Addiction and Substance Use Disorders, Restless Legs Syndrome, Schizophrenia and Huntington’s Disease.

Catalog

Warnimgs:

The following appears to reduce dopamine

Lacticaseibacillus casei LA205 and Lacticaseibacillus paracasei LA903 REDUCES Dopamine [2023]

Lactobacillus delbrueckii  [2021]

Lactobacillus plantarum DR7 [2019] but increases serotonin 

Bifidobacterium CECT 7765 [2017]

Psychoactive Probiotics! – 2024 Update for GABA

A reader asked me to do an update of my 2016 post Psychoactive Probiotics! There has been a lot of recent literature as shown on PubMed. Note that often these are strain specific and not generalized for species cited below. If you cannot find the strains specified in the studies, it may be worthwhile trying different brands of the species (with the most studied species being most probable).

Excessive GABA may be associated with Huntington’s disease, epilepsy, and certain types of encephalopathies. Insufficient GABA may be associated with Anxiety Disorders, Epilepsy, Sleep Disorders, Mood Disorders, Substance Use Disorders, Movement Disorders, Neuropathic Pain and Autism Spectrum Disorders.

“Metagenomic analyses suggest that the genomes of many gut bacteria encode glutamate decarboxylase (GAD), the enzyme that catalyzes GABA production.” [2023]

“Stress exposure induced a decline in Lactobacillaceae abundance and hence γ-aminobutyric acid (GABA) level in mice.” [2023]

Note: monosodium glutamate (MSG) can increase the production of GABA [2024]

Effect of Probiotic Therapy on Neuropsychiatric Manifestations in Children with Multiple Neurotransmitter Disorders: A Study[2023] The results indicate that psychobiotics have a significant impact on reducing hyperactivity and aggression, and improving concentration

Probiotic Catalog

NOTE: The current official name is used below. Most L. species were known as Lactobacillus with older names.

Note: Gamma aminobutyric acid production by commercially available probiotic strains [2023] cites that the best are: Levilactobacillus brevis LB01 [Source], Lactiplantibacillus plantarum 299v [Jarrow Formulas Ideal Bowel Support].

Lactiplantibacillus plantarum 299v is the most available with many suppliers. A dosage of 10-60 BCFU per day is recommended.

Allergies, Asthma, CFS – then a semi-miracle.

Backstory

I think I grew up with dysbiosis, as evidenced by allergies, mild asthma, and neuro divergencies (extremely withdrawn and attention deficit). In my 20s developed mild semi-functional CFS due to chronic stress.

In 2020 was exposed to black mold, and had a short very strange illness around this time. Then later I got the first 2 covid vaccines, followed by the booster Dec 2021, which was my major trigger.
Symptoms: Shortness of breath, CFS, chest pain,chest pressure, palpitation, insomnia, fight or flight/anxiety, hallucinations, joint pain, food intolerance, histamine issues, exercise intolerance, PEM, tinnitis, nausea, apparent veinous insufficiency, endotheliatis head pressure, neck pain, POTS, etc. I also grew a nerve tumor (this appeared 2 years later). EBV antibodies showed very high.

Some of these symptoms have gone away, and my intensity of illness is maybe 1/3 of what it was in the beginning, but I seem to have reached a plateau. My Biomesight showed a bunch of issues and I’m looking to correct it in order to give my immune system a chance to normalize.

Analysis

We see an excessive number of bacteria/taxa at very high levels, suggesting they are dominating the microbiome.

Drilling down to Health Indicators

With Dr. Jason Hawrelak Recommendations, we are at the 66%ile, a reasonable level.  The MHI-A ratio is low, indicating issues. With Bacteria deemed Unhealthy, Streptococcus vestibularis(An unhealthy Predictor) was at 98%ile and Escherichia coli was at 96%ile. E.Coli can be good or bad (16s is not able to tell them apart) — an ad-hoc test is to try Mutaflor probiotics (E-Coli Nissle 1917) and if there is either a major herx or major improvement, then we can assume a major bad E.Coli component. Mutaflor is aggressive against bad E. Coli.

Using Potential Medical Conditions Detected, one items is a strong match: Postural orthostatic tachycardia syndrome at 85%ile

Using the new Taxa-Symptom Association, we find some strong matches at the order level, which are not there at the genus level. The highest possible factor is 100 (matching every association).

For information on this feature see: Evolution of Addressing Microbiome/Gut issues which includes a video.

Looking at Black Mold, Prevotella growth is associated with mold. We are relatively high, 81%ile. Associations of observed home dampness and mold with the fungal and bacterial
microbiomes
[2021]. However, the mold in the environment predictor is at the 30%ile. General advice is to check (and test) for mold in home and work environment; keep humidity low in both.

Scanning General Health Predictors, the only item that stood out was low Vitamin K2 production, which suggests that Vitamin K supplements may be beneficial.

Going Forward

I am going to do [Just Give me suggestion with symptoms] and then suggestions using Order above (the taxa rank that has the highest factor (best match)]. This gives us 6 sets of suggestions. Taxa “Order” is above the data for antibiotics, so sorting to only those items with 6 Takes, we end up with a clean list shown below of all suggestions saying take with high Priorities — sweet!. Lactobacillus casei, siblings (paracasei) and lactobacillus casei shirota (probiotics) dominate probiotics to the exclusion of other probiotics. This group is well known to help allergies and reduce histamine issues.

Items to Take

Priority  ModifierModifier Type
554.7lactobacillus casei (probiotics)Probiotics
499.6CurcuminHerb or Spice
496.6vitamin B3,niacinVitamins, Minerals and similar
485.8garlic (allium sativum)Herb or Spice
479.1Hesperidin (polyphenol)flavonoids, polyphenols etc
469.2lactobacillus paracasei (probiotics)Probiotics
445.9Vitamin B1,thiamine hydrochlorideVitamins, Minerals and similar
443.1Arbutin (polyphenol)flavonoids, polyphenols etc
443.1diosmin,(polyphenol)flavonoids, polyphenols etc
443.1luteolin (flavonoid)flavonoids, polyphenols etc
443.1retinoic acid,(Vitamin A derivative)Vitamins, Minerals and similar
443.1Theobromine (in food)Prescription – Other
443.1Vitamin B6,pyridoxine hydrochlorideVitamins, Minerals and similar
407.2Vitamin B-12Vitamins, Minerals and similar
403tannic acidHerb or Spice
395soyFood (excluding seasonings)
385.1melatonin supplementAmino Acid and similar
327Guaiacol (polyphenol)flavonoids, polyphenols etc
324.2schinus molle (herb)Herb or Spice
302sesuvium portulacastrum herbHerb or Spice
300.5lactobacillus casei shirota (probiotics)Probiotics
298.3tabebuia impetiginosa (taheebo) barkHerb or Spice
283.7CaffeineFood (excluding seasonings)
278.9wheyFood (excluding seasonings)
277.4Human milk oligosaccharides (prebiotic, Holigos, Stachyose)Prebiotics and similar
271.9teaFood (excluding seasonings)
262.3low-fat dietsDiet Style
254.6lactoseSugar and similar
251.8vitamin B7, biotinVitamins, Minerals and similar
246.7chitosan,(sugar)Sugar and similar

Items to Avoid

At the other end, only a few items were on the to avoid for all 6 sets of suggestions.

Priority  ModifierModifier Type
-443.8oligosaccharides (prebiotic)Prebiotics and similar [6]
-411.1BofutsushosanHerb or Spice [6]
-403.4non-starch polysaccharidesSugar and similar [6]
-340.6Slippery ElmHerb or Spice
-335.8bacillus coagulans (probiotics)Probiotics [6]
-334.4arabinogalactan (prebiotic)Prebiotics and similar
-314.7lupin seeds (anaphylaxis risk, toxic if not prepared properly)Food (excluding seasonings)
-301.7carobFood (excluding seasonings)
-298.3levanSugar and similar
-289.2PulsesFood (excluding seasonings)
-276.2l-prolineAmino Acid and similar
-254.6macrolide ((antibiotic)s)Antibiotics, Antivirals etc
-252.8vegetariansFood (excluding seasonings) [6]
-252.5Bile Acid SequestrantMiscellaneous, food additives, and other odd items
-247.9dietary phytoestrogens (isoflavones)Diet Style
-245.6pectinFood (excluding seasonings)
-241.7barley,oatFood (excluding seasonings)
-241.7resistant maltodextrinPrebiotics and similar
-236.3amaranthFood (excluding seasonings)
-235.3fastingFood (excluding seasonings)
-232.6Dendrobium officinaleHerb or Spice
-226.2fruit/legume fibreFood (excluding seasonings)
-221.1Ferric citrateVitamins, Minerals and similar
-220.7xylan (prebiotic)Prebiotics and similar
-218.8disodium fumarate (food additive)Miscellaneous, food additives, and other odd items
-216.5dairyFood (excluding seasonings)
-216.3Olive OilDiet Style
-215.4vsl#3 (probiotics)Probiotics
-212.1high-fat sucroseFood (excluding seasonings)

Bottom Line

I was also a person who responded very well to Mutaflor (we always have some in the fridge). In my case, the initial response was massive herxing for two weeks.

General Guidance

For items to take, remember that goal is to disrupt the dysbiosis. This means subjecting it to constantly changing “shocks” so it is unable to adapt. This has been shown to be effective when dealing with antibiotics (i.e. rotating between different antibiotics with breaks is more effective than taking the same antibiotic continuously).

My suggestion for a rotating 4 week cycle changing probiotics and herbs every week. Be aware of not falling into either the homeopathic or product labelling traps — that is, taking less then therapeutic levels. To determine those dosages see Supplement Dosages. In general, you want to be close to the maximum dosages used in studies (i.e. “deemed safe dosages”).

Vitamins and polyphenols can be taken continuously.

Feedback

Honestly, whatever algorithm is being used for symptoms is nothing short of amazing 

POTS is probably my main challenge, and I have all but two of the other symptoms. And the two that I don’t currently have (joint pain and insomnia) I have had in the past. So basically it’s 100% accurate in my case

For interventions- A friend of mine just mentioned diosmin to me the other day. B3, B1, HMO, caffeine have all  been helpful. Amazed to see Curcumin so high as it’s not really something I considered trying. 

Mutaflor has been amazingly helpful the last few days (neurotransmitters and gut and fatigue) but I’ve heard it can’t be taken with other probiotics due to competing?

I’m interested in Lactulose for the bifido also, as I’ve heard a lot about this recently..  Thanks for taking the time, very very interesting!
Also, one question if you have a moment. Are the interventions supposed to – directly improve the biome Or improve symptoms?

From first draft sent to him.

Answer: The data is computed to correct the bacteria shifts with statistical associations to symptoms. Adding suggestions for symptoms is another massive data extraction and entering. Readers can do cross validation for symptoms if they are inclined to search the literature (https://pubmed.ncbi.nlm.nih.gov/ )

Here’s an example: https://blog.microbiomeprescription.com/2023/02/12/cross-validation-of-ai-suggestions-for-nonalcoholic-fatty-liver-disease/

Many suggestions have never been tried against the symptoms.

Q: Or can the herbs possibly be mixed w probiotics?

  • Yes they can, but you should check that the herb does not inhibit the probiotics currently being taken. To do this, just click on the herb, You want compatible probiotics with the herbs.

Q: Also, do your algorithms pick up probability of sleep apnea and cancer? These are conditions I’m trying to assess my risk of having / getting 

  • They do pattern matching by two methods:
    • Articles on the US National Library of Medicine (go to https://microbiomeprescription.com/Library/PubMed ) AFTER LOGGING IN. It gives the percentile ranking of the number of matches you have compare to other samples.
    • Citizen Science based on self-reported symptoms and diagnosis. At present only Sleep Apnea Diagnosis has sufficient data for biomesight samples. For Sleep Apnea, you have 63% of the shifts matching which suggests that you may be heading in that direction, but sleep disturbances have much higher matches.

Q: This is extremely helpful Do you have any idea if there would be an interaction between mutaflor and lactulose? Mutaflor has still been amazing , semi- miraculous. It’s working so well I haven’t tried anything else yet. But I am very keen to get my bifido up 

A: It’s an easy lookup on the site. https://microbiomeprescription.com/library/modifier?mid2=1709  and it links to 2 studies which reports it.


Postscript – and Reminder

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

I cannot tell people what they should take or not take. I can inform people items that 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 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.Posted on  by Research and tagged 

Eubiosis Revisited

Recently I have gotten some messages concerned about Eubiosis scores dropping. Eubiosis is a measure of evenness of the bacteria representation. It cannot be used to identify which bacteria needs to be changed. It is a representation of the Chi2 value of the genus converted to %ile with values over 80%ile deemed 100%.

What is statistically ideal is:

Below is an example of a low score of 1.2%

Dr. Jason Hawrelak score is 28%ile, MHI-A Ratio is 47%

It is saying that you have very few bacteria genus that have high representations and a ton of bacteria with high representation. This patterns suggest that the gut has become destabilized (which if you have dysbiosis is a good thing) but has not stabilized.

Same Person – Prior Pattern

The person has improved compared to this pattern. The “peak: was at 10-19 and above it has shifted to 10-29 range. Dr. Jason Hawrelak score is 46%ile MHI-A Ratio 67%

Same Person — further back

This is a better looking pattern. But remember this is not a primary measure for a gut score, but an adjunct dimension to be considered. For example, Dr. Jason Hawrelak score is a low 5%ile. MHI-A Ratio 66%ile

Bottom Line

There is no single number that represents an accurate gut health score. DO NOT DEEM EUBIOSIS to be such. It should be considered with items like: Dr. Jason Hawrelak score at least, and MHI-A Ratio ( see Development and Validation of a Novel Microbiome-Based Biomarker of Post-antibiotic Dysbiosis and Subsequent Restoration). Microbiome Prescription gives a multitude of different numbers estimating gut health based on literature, or in this case, statistics.

Gender based Microbiome Shifts for ME/CFS and other conditions

A question was ask – are there significant gender differences with ME/CFS. A partial answer is possible from our citizen science data (Available here). The number of bacteria identify as statistical significant drops because we are reducing sample sizes. The table below shows the shifts that are seen in common with P < 0.01.

For Symptom of ME/CFS

SourceTax_nametax_rankMaleFemaleMale_Chi2FeMale_Chi2
thryveThermodesulfobacteriaphylumincreasesincreases234.0375138.4544
biomesightVerrucomicrobiaceaefamilyincreasesincreases8.3333337.262051
biomesightRhodothermaeotaphylumincreasesincreases179.2217.3071
biomesightAkkermansiaceaefamilyincreasesincreases8.7183789.965634
biomesightErysipelothrix murisspeciesincreasesincreases9.53388910.08333
biomesightAkkermansiagenusincreasesincreases8.7183789.965634
biomesightRhodothermalesorderincreasesincreases179.2217.3071
biomesightAkkermansia muciniphilaspeciesincreasesincreases8.7183789.965634
biomesightErysipelothrixgenusincreasesincreases9.6632899.663289
biomesightRhodothermiaclassincreasesincreases179.2217.3071
biomesightThermodesulfobacteriaphylumincreasesincreases281.1738299.9112

ME/CFS With IBS

We find differences here.

SourceTax_nametax_rankTaxonMaleFemaleMale_Chi2FeMale_Chi2
biomesightSutterellagenus40544decreaseincreases8.33333311.25018
biomesightRhodothermalesorder1853224increasesincreases139.9274114.5716
biomesightDoreagenus189330increasesdecrease18.7516.17875
biomesightRhodothermiaclass1853222increasesincreases139.9274114.5716
biomesightThermodesulfobacteriaphylum200940increasesincreases280.3333187.9779
biomesightSutterellaceaefamily995019decreaseincreases8.33333311.25018
biomesightAlcaligenaceaefamily506decreaseincreases8.3333339.120714
biomesightRhodothermaeotaphylum1853220increasesincreases139.9274114.5716

ME/CFS Without IBS

We found no differences yet (given the sample size)

SourceTax_nametax_rankTaxonMaleFemaleMale_Chi2FeMale_Chi2
biomesightBacteroides fluxusspecies626930increasesincreases7.3551617.910588
biomesightThermodesulfobacteriaphylum200940increasesincreases124.4571170.4624

Irritable Bowel Syndrome

Following up from above and noting that there is a gender bias in incidence, we find some differences

thryveThermodesulfobacteriaphylum200940increasesincreases252.823295.10095
biomesightRhodothermalesorder1853224increasesincreases125.1467110.6182
biomesightRhodothermiaclass1853222increasesincreases125.1467110.6182
biomesightThermodesulfobacteriaphylum200940increasesincreases314.4971174.6182
biomesightRhodothermaeotaphylum1853220increasesincreases125.1467110.6182
biomesightSharpea azabuensisspecies322505increasesincreases16.185266.80625
biomesightSharpeagenus519427increasesincreases16.185266.80625
thryveMycoplasmagenus2093increasesdecrease12.8152420.3229
thryveMycoplasmataceaefamily2092increasesdecrease14.8858120.3229
thryvePhocaeicola vulgatusspecies821increasesdecrease7.89349217.06273
thryveMycoplasmatalesorder2085increasesdecrease14.8858126.01485

Depression

Another condition with a gender association

SourceTax_nametax_rankTaxonMaleFemaleMale_Chi2FeMale_Chi2
thryveThermodesulfobacteriaphylum200940increasesincreases227.7557148.4336
thryveParabacteroides distasonisspecies823decreaseincreases9.11835613.46941
thryveEubacterium oxidoreducensspecies1732decreaseincreases12.995076.76
biomesightRhodothermalesorder1853224increasesincreases121.200291.125
biomesightRhodothermiaclass1853222increasesincreases121.200291.125
biomesightThermodesulfobacteriaphylum200940increasesincreases223.4402189.2431
biomesightRhodothermaeotaphylum1853220increasesincreases121.200291.125
thryveLactobacillus rogosaespecies706562decreasedecrease23.8836812.12781

Symptom: Problems remembering things

This is one of the characteristics of ME/CFS, Long Covid, etc

SourceTax_nametax_rankTaxonMaleFemaleMale_Chi2FeMale_Chi2
thryveThermodesulfobacteriaphylum200940increasesincreases316.4446120.0944
biomesightRhodothermalesorder1853224increasesincreases171.7445133.3333
biomesightRhodothermiaclass1853222increasesincreases171.7445133.3333
biomesightThermodesulfobacteriaphylum200940increasesincreases369.0078289.0992
biomesightOdoribacteraceaefamily1853231increasesincreases12.793117.962632
biomesightRhodothermaeotaphylum1853220increasesincreases171.7445133.3333
biomesightAcetivibriogenus35829decreaseincreases9.18086517.49208
biomesightOdoribactergenus283168increasesincreases9.33494912
biomesightAcetivibrio alkalicellulosispecies320502decreaseincreases9.18086519.95636
biomesightHathewaya histolyticaspecies1498decreaseincreases9.1808657.262051
biomesightHathewayagenus1769729decreaseincreases9.1808657.262051
biomesight[Clostridium] thermoalcaliphilumspecies29349increasesincreases7.356.880909
thryveIntestinimonasgenus1392389decreaseincreases168.552727
thryveIntestinimonas butyriciproducensspecies1297617decreaseincreases16.486469.992258
ubiomeBacteroides sp. EBA5-17species447029increasesdecrease9.0555777.314286

Symptom: Worsening of symptoms with stress.

Another common symptom of ME/CFS

SourceTax_nametax_rankTaxonMaleFemaleMale_Chi2FeMale_Chi2
thryveThermodesulfobacteriaphylum200940increasesincreases282.4023185.22
biomesightThermoanaerobacterales Family III. Incertae Sedisfamily543371decreaseincreases22.004548.491649
biomesightSharpeagenus519427increasesincreases17.5562512.38345
biomesightHathewayagenus1769729decreaseincreases16.9861211.70814
biomesightRhodothermalesorder1853224increasesincreases142.9353188.8704
biomesightHathewaya histolyticaspecies1498decreaseincreases16.9861211.70814
biomesightSharpea azabuensisspecies322505increasesincreases17.5562512.97965
biomesightRhodothermiaclass1853222increasesincreases142.9353188.8704
biomesightThermodesulfobacteriaphylum200940increasesincreases352.2616362.7038
biomesightAcetivibrio alkalicellulosispecies320502decreaseincreases12.658188.491649
biomesightRhodothermaeotaphylum1853220increasesincreases142.9353188.8704
biomesightAcetivibriogenus35829decreaseincreases12.658188.491649

Other Symptoms with Significant Gender Differences in patterns

  • Immune Manifestations: Abdominal Pain
  • Sleep: Unrefreshed sleep
  • Comorbid: High Anxiety
  • General: Fatigue
  • Neurological-Audio: hypersensitivity to noise
  • DePaul University Fatigue Questionnaire : Unrefreshing Sleep, that is waking up feeling tired
  • DePaul University Fatigue Questionnaire : Fatigue
  • Neurocognitive: Brain Fog
  • Neurocognitive: Problems remembering things
  • DePaul University Fatigue Questionnaire : Anxiety/tension
  • General: Myalgia (pain)
  • Immune Manifestations: Constipation
  • Post-exertional malaise: Rapid muscular fatigability,
  • Neuroendocrine Manifestations: Poor gut motility
  • Comorbid: Restless Leg
  • Comorbid: Small intestinal bacterial overgrowth (SIBO)
  • DePaul University Fatigue Questionnaire : Difficulty finding the right word
  • DePaul University Fatigue Questionnaire : Mood swings
  • DePaul University Fatigue Questionnaire : Pain in Multiple Joints without Swelling or Redness
  • Sleep: Problems falling asleep
  • Sleep: Problems staying asleep