Author: Research

Report Targeted to MD in Multiple Languages

A common complaint that I have heard is a lack of knowledge about the microbiome by treating MDs. This issue is compounded by MDs allowing only 10-15 minutes appointments. Many of complaints are from EU Countries where their MD have limited mastery of English.

This reported is targeted for those MDs using the following strategy:

  • A short section of what should be substances should be tried to be reviewed by the MD.
    • Every item is linked to one or more studies where it was found helpful for some people (responders)
    • Every item is linked to the bacteria that it changes
  • A break down of all bacteria out of range according to studies on this condition, with links.
  • A detail cross reference on the bacteria that each substances. The goal is to encourage MDs to insure at least one substance is advocated for each bacteria
  • A long list of the studies cited. This list is intended to overwhelm the MD with evidence. One or two studies is easy to dismiss for many MDs. A long list is hard to dismiss psychologically..

How do I get this Report?

Assuming you have transfer or uploaded a sample to Microbiome Prescription, go to the [Changing Microbiome] tab. You will see your samples (and the active one). Below it is this section:

Pick the preferred language. Click the conditions you have. Click Get Report. If your condition is missing, see the bottom of this post for why and how you can change this.

How this Report is different

This uses a strictly “by the medical book” analysis and will likely generate some suggestions different from other reports on the site. This is required to be able to do cross references for every item.

Typical Knowledge Section

This is actually coming from ChatGPT and is a likely match to the MD’s “common sense”

Bacteria Being Targeted

This is next because we want to explain WHY we are making suggestions before presenting them.

Substances to Consider

This list may be long or short (depending on conditions). Many MDs will likely be happy with most of these suggestions. For those that they are unsure about, we have a link to studies that may persuade them over time.

Substance Impact on Bacteria

This is intended for MD education. It illustrates that the microbiome can be manipulated and there are lots of studies.

Additional Suggestions

This is intended to be a carrot for the MD to learn more.

References

This speaks for itself, and that the suggestions are well researched.

Why is your Condition not listed?

The simple reason is that someone has to diligently go through the literature to assemble all of the information by hand. Often a report will have more than 600 citations – that’s a lot of work. For Autism, some parents did the work and this we have a report for autism. If you are interested in doing this research for your missed condition(s) see Help Needed to Improve Suggestions for Autism. for the steps needed.

Just Identifying the Bacteria for more conditions….

Bottom Line

This report was engineered by trying to walk in the mind frame and world of the MD. Speak to him in his preferred language and way of thinking.

Enhancement: Amount of Biofilm Bacteria

A reader in Europe asked about this. I know it is a popular topic. So, I searched PubMed for the known biofilm forming bacteria and will be adding percentile ranking by labs in the coming days.

Raw Count Chart

As you can see below — a lot of people have ZERO of these bacteria. Other people may have 25% of their microbiome containing them. IMHO, influencers have seized on this concept as a “boogey man” for every one; it is not.

Transforming the data to get a Kaltoft-Moldrup estimator of the point of concern, we get a count of 565/million or 0.0565% being the threshold that action is strongly suggested. That is, with 85% of samples, it does not appear to be a significant issue. For 15%, it is

Stay tune. It will be added to the health analysis page with suggestions annotated with possible biofilm breakers for people exceeding 80%ile.

ME/CFS post EBV

Back story

I have a longstanding history with ME/CFS from 2006 – diagnosed with EBV at the time

The primary concerns are: fatigue, PEM, brain fog, exacerbation of symptoms prior to menstrual cycle (PMDD), ADHD, POTS (improving), anxiety, PCOS. The fatigue and PEM is the main concern. Many other symptoms recently improved. 

I’m currently taking L. rhamnosus, D-ribose, methylated B-complex, berberine, maitake, magnesium citrate, copper niacin and started myo-inositol after submitting the sample. I was also taking saccharomyces boulardii for weeks leading up to the sample collection. I’ve discontinued it since then. I would like to change my diet in general, but first want to see what’s recommended. Also particularly unsure about oxalates and whether or not to continue the maitake mushroom.
I’m also curious to try oxaloacetate,

Interestingly enough, I had rather extreme vaginal discharge and discomfort for many months, which completely went away within a couple of weeks of using a probiotic mix. I stopped this probiotic (it had 7 strains, I believe) and the discharge has not returned, although fatigue is worse (but other things also changed).

Analysis

The graphic overview is shown below. There are clearly a group of bacteria that are overgrown (70-89%ile) and other bacteria that rarely have token representations (0 -29%ile). This does not identify the bacteria but identifies misrepresentations (thus dysbiosis)

Looking at General Health Predictors, we see 12 items of concern, higher than seen in most reviews. Both Oxalate degrading and Oxalate producing at below 1%ile. Dr. Jason Hawrelak criteria came in at 78%ile

We have quite a number of bacteria strongly statistically associated symptoms and others associated with with health risks.

Going Forward

Where there are many issues wrong, I do not attempt to work bacteria by bacteria — instead, I trust the expert system to consider and balance all of the factors in a consistent and logical method. This is especially with the revised algorithm (see Algorithm for “Just Give Me Suggestions” with symptoms) . It inherited included items that in the past I have done as extra suggestions.

I have recently added new option to make the analysis simpler.

Items to Take

Today, I am working on several other posts from ME/CFS and the suggestions here are very similar to those suggestions (just different orders). Spices and herbs can be done as capsules, teas, oils or just putting on food.

Modifier To Take
whey
whole-grain barley
oregano (origanum vulgare, oil)
clostridium butyricum (probiotics),Miya,Miyarisan
syzygium aromaticum (clove)
thyme (thymol, thyme oil)
rosa rugosa
lactobacillus kefiri (NOT KEFIR)
lactobacillus paracasei (probiotics)
galla rhois
neem
garlic (allium sativum)
bifidobacterium animalis lactis (probiotics)
bifidobacterium infantis,(probiotics)
Shen Ling Bai Zhu San
lactobacillus casei (probiotics)
foeniculum vulgare,fennel
momordia charantia(bitter melon, karela, balsam pear, or bitter gourd)
triphala
mastic gum (prebiotic)
vitamin b2,Riboflavin
aloe vera
sucralose
soy

Looking at probiotics, we have a good number that would allow easy rotation of probiotics. Two are usually difficult to obtain: lactobacillus kefiri and lactobacillus sakei . Most are available at my usual two preferred sources: Custom Probiotics and Indian Bulk Exporter (Maple Life Sources). See this list for sources not available there. By rotation, I mean 20-50 BCFU daily of one probiotic for 2 weeks and then change to another probiotic.

lactobacillus kefiri (NOT KEFIR)
lactobacillus casei (probiotics) [CB,MLS]
lactobacillus sakei (probiotics)
bifidobacterium animalis lactis (probiotics) [CB,MLS]
lactobacillus reuteri (probiotics) [CB,MLS]
bifidobacterium infantis,(probiotics) [CB,MLS]
enterococcus faecium (probiotic)
lactobacillus paracasei (probiotics) [CB,MLS]
clostridium butyricum (probiotics),Miya,Miyarisan

Items to Avoid

Modifiers To Avoid
Slippery Elm
non-starch polysaccharides
xylan (prebiotic)
levan
l-citrulline
berberine
schisandra chinensis(magnolia berry or five-flavor-fruit)
low-fat diets
blackcurrant
symbioflor 2 e.coli probiotics
red wine
alcoholic beverages
animal-based diet
stevia
red alga Laurencia tristicha
high sugar diet
  • proton-pump inhibitors (prescription)

Suggestions look very “old-school ME/CFS”

By old school, I mean what was reported to help most people on the ancient egroup list CFSFMExperimental. Namely:

  • Whey (non-denatured was thought the best)
  • B-Vitamins
  • Bidifobacteria probiotics (little Lactobacillus)

For all items, I would suggest checking for sufficient therapeutic dosages here. The dosages on bottoms usually are maintenance and insufficient to be therapeutic. Example: Neem at 120mg/day which is 3 “00” capsules per day (just measured it!). Garlic is 4 grams per day – typically 4 commercial 1000mg capsules per day (double or more of the dosages on bottles). As you can see below, recommended dosages may be just 1/3 of that.

My general rule of thumb is 1 “00” capsule with each meal for most herbs. We make our own capsules using organic powders without fillers. Cheaper and better quality than commercial pills.

Remember, with herbs and probiotics you do not want to take the same one continuously. Take each set for 1-2 weeks and then rotate to another. For example

You should check each to see if they have adverse effect on whatever probiotics you may take concurrently. For example Shen Ling Bai Zhu San and rosa rugosa both are reported to increase Bifidobacterium — so taking Bifidobacterium with them is fine.

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.

Why sites suggestions disagree on the same data

A reader wrote:

There’s one thing I which caused some bewilderment though,  I put the screenshots from the recommendations from Biomesight here below, and I don’t understand why they seem quite divergent to what you are suggesting. I don’t know if it’s just my amateur eyes and then not so divergent after all, but to me they do seem quite different (apart from the lactobacilli). Shall I just ignore their suggestions ( also food wise) or would you say by and large it goes into the right direction? 

Reader, May 23,2024

The answer depends on the logic each provider uses, which bacteria are in their microscope that needs changes, depth of their research and their skills in addressing contradictory results. I will look at three providers below:

  • Biomesight (provided by the reader)
  • Startup in US(from a review copy)
  • Microbiome Prescription

See also this post: Why do metabolite levels disagree between sites?

Biomesight

We see a number by each suggestion

Hovering over the item will show the bacteria believed to be impacted

Clicking on the name will show details. Note that the bacteria shown is correct. The link also shows “Galactooligosaccharides (GOS)” and not the food suggested explicitly. The food selected contains GOS but none of the studies are explicitly for Beetroot. To MP, the beetroot contains multiple compounds, some may have overpowering negative effects — hence MP keeps to precisely what is cited in the study.

My inferred take-away from looking at the suggestions

  • Foods and substances are done by association and inference
  • Only a handful of bacteria are considered.

Consider the bacteria list on MP for the same substance – 1757 citations at the moment.

New Start-up

This is from an early draft. They are using the database of Microbiome Prescription but with a set of proprietary rules, custom ranges, and algorithms. They restrict their scope to a few dozen genus. For the bacteria in their scope, MP has no contraindicated data and do not use inferences to parent or child taxa. That is, there is no need for balance algorithms. In short, it is a proprietary suggestion system designed.

Microbiome Prescription

For details on which bacteria are selected, see Algorithm for “Just Give Me Suggestions”. Typically we have an average of 65 bacteria under our microscope with 600 on some shotgun samples. Roughly 20-30% of the bacteria identified.

Now for every suggestion we make available the list of studies (137 for this probiotic suggestion). Note in the study names — that this probiotic is explicitly named.

We also include the negative effects

We have our own proprietary algorithm on how to evaluate this data. People can take this data and apply their own logic.

MP’s goal is to be the most comprehensive source with new studies adding every week. We have also been delighted that the startup (who I have been doing pro-bono consultation with) have set a team of their M.Sc. (or higher) staff on checking the citations. They have been finding a very low bad entry rate ( < 1%) but discarding 8% of studies for diverse reasons. The startup criteria (no contradictory results from different studies) often result in only 10% of available studies being used.

Bacteria Selected Determine Suggestions

Microbiome Prescription does NOT know what is the best method of picking bacteria to focus on. The Simple UI gives THREE different approaches.

  • Novice works on anything out of range – often including harmless bacteria in the calculation.
  • Beginner – Symptoms: Works off patterns of bacteria associated to user reported symptoms that are statistically significant
  • Beginner-Diagnosis: Bacteria shifts reported associated to diagnosis in published studies.

It is possible that the bacteria selected by each of these method will have no overlap. IMHO, Beginner – Symptoms is the most likely to be correct. THE BACTERIA SELECTED DETERMINE THE SUGGESTIONS.

For more advance users, there are a lot more (84x) methods of picking bacteria:

Regardless of method, if you go to Consensus Report

You will see PubMed with stacks of books under it. Just click on the books

This shows the studies used and the logic

Best practice is to always save the page as a PDF and the Consensus View as a CSV. Often people will come back later and see different suggestions because they selected a different method of picking bacteria. One other factor is that data is added weekly to the database which will cause shifts over time.

Bottom Line

  • What is the scope of their microbiome scope? IMHO: the bigger the scope, the better the results
  • Is the data based on explicit studies or on interference (A contain X and X helps — we’ll ignore B,C,D that is also in X)
    • BEWARE of sites that do not provide explicit studies – often they are working from hearsay.
  • Does the suggestion consider contraindicated information?
  • How big a database are they using? Have there been third party checking of the database?

Suggestions may be reasonable: a professional dietician would likely do the same logic in the case of BiomeSight suggestions.

Questions

  • Since Startup and Microbiome Prescription use the same database, will suggestions always agree?
    • No, for several reasons:
      • The bacteria in-scope-to-change are different. If MP picks one that Startup does not, then suggestions may shift for some substances. Startup computes its own definitions of what is high and low. They also look at a handful of genus only.
      • Startup hand select certain studies to be excluded or lessen in values. Studies may be on human, animals or a lab situation (petri dish) – they wanted to weight the value of each study different from MP.
  • What should I do if there are explicit disagreements?
    • The safest path is to do only things that there is agreement on.
    • If another item interests you, review the studies cited to make a decision.

Multiple COVID Infections… ouch

Backstory

I had no gut problems and only minor health niggles before Covid. I have been hypothyroid for 20 years.

After three rounds of covid (but no vaccines) I have burning and tingling parasthesias in my extremities, neuropathy in my face, plus gut pain, lots of hair loss, and I feel cold a lot and sleep poorly. Some fatigue and shortness of breath, but the other symptoms are much worse.

Trying to increase my bifido and lactobacillus via suggestions on biomesight has barely moved the needle.

All my blood tests work has been normal from a year ago, although now I have a weakly postiive ANA test result.

Analysis

We have 2 samples: 2023-11-20 and 2024-04-26. Both samples are very similar.

High Level Overview

Looking at the “smoking gun”, Pedobacter, we found no known factors to reduce it 🙁

Quick Summary; Past action plan has “barely moved the needle.”

Going Forward

The usual “just give me suggestions” with one addition Bifido and lactobacillus are her primary concern, so I will hand picked those on both samples. and get an emphasis for thoses. We see that one went up and one went down.

Bacteria20242023
Lactobacillus (only Lactobacillus iners)38%ileNONE
Bifidobacterium8%ile39%ile

We then do a Uber Consensus with BOTH samples (since they are similar) with a total of 11 sets of suggestions.

  • All 11 agrees on these:
    • bifidobacterium animalis lactis (probiotics)
    • vitamin a
    • Olive Oil
    • barley
    • lactobacillus brevis (probiotics)
    • clostridium butyricum (probiotics),Miya,Miyarisan
    • ginger and rosemary
  • Items to be avoided on all 11 are below
    • lactobacillus gasseri (probiotics)
    • chitosan,(sugar)
    • vegetarians
    • blackcurrant
    • Dextrin
    • Guaiacol (polyphenol)

I looked at the interaction charts, the first one is for Lactobacillus and noticed high (99%ile) for Rickettsia and for Heliobacter (61%ile). The last one suggests testing for Helicobacter pylori should be discussed with their MD.

The chart for bifidobacterium shows many of the same bacteria that will surpress bifidobacterium. Note that lactobacillus (top right) is indicated as surpressing bifidobacterium; this agrees with the above numbers.

This appears to illustrate that being focused on just one or two bacteria may not be the best path. A holistic approach (looking at what changes all of the bacteria above may be a critical step of improving things).

Antibiotic path

Long COVID is very similar to ME/CFS. Looking at antibiotics suggestions, about 60% of them are commonly use bt ME/CFS specialists. These areL

My personal preference would be one round of metronidazole, a three week break then minocycline, another break and then one of the other ones. This is following Dr. Jadin’s Current Protocol for ME/CFS using antibiotics

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.

Multiple Chemical Sensistivity With Mast Cell Issues

Back Story

I’m at the end if my rope and need help. I’m at my wits end with:

  • mcas and
  • mcs.

I was hit by levaquin in 1/14/20. It killed off my microbiome 22 days later reactions started. I believe has Sibo since then but was confirmed 4/23 and 4/24: Methane and hydrogen

I started raw milk one year ago and was able to stop food and scent reactions I was 85% better until March when dryer sheets on someone I m home set me off then a true anaphylactic event on 4/1 needing epi pen. Since raw milk I developed sulphur intolerance

I’m miserable and like ready for assisted suicide… but not seriously. I can’t deal with it anymore the ecoli albertii is way high 97% higher than everyone who took Biomesight so is methanobacter smithii I can’t tolerate any of the sulphur products since raw milk over grew stuff making me sulphur sensitive to microbes releasing sulphur. I never had issues with sulphur before raw milk one year ago!!!! I used to soak in Epsom all the time and eat garlic and broccoli like crazy that all stopped with this over growth!!!

My mast cell reactions and brain fog are once again bad. I do have mthfr do it’s hard to detox not sure that matters

Initial Analysis

As a start point, this has the lowest eubiosis that I have reviewed. Eubiosis is a computation on the chart below it. We see a lot of different species at abnormally high levels. A balance gut would have all of the blue lines close to the red lines.

There are a number of these bacteria that are strongly associated statistically with different symptoms.

I added the symptoms cited and went over to the new “Symptoms associations to Taxon, Compounds and Enzymes” to give this new feature an actual data case.

Comorbid: Multiple Chemical Sensitivity

Checking Enzymes for other conditions for possible vitamin impact.

Oral Bacteria Leakage

Looking at this new feature, we see three bacteria that stand out.

I did a hand-picked suggestions on just these three to see what can likely be done:

I went to another person that used the same lab that I know with both of these conditions and we see something in common

The LLM comment stated: Metabolic Interactions: Some Veillonellaceae bacteria, including Dialister species, are known for their metabolic interactions with other bacteria in the microbiota. They can metabolize certain compounds produced by other bacteria…

Going Forward

I am going to do “Just give me Suggestions include Symptoms” with the revised algorithm (see Algorithm for “Just Give Me Suggestions”) . I could have hand picked each bacteria associated with symptoms, but given the number of very high, this would likely produce similar effect with less effort.

This results in the Consensus having 7 sets of suggestions

Suggestions To Take

The top, non-prescription items are below. It is full of spices and herbs with just one vitamin and one probiotic.

Modifier
cinnamon (oil. spice)
oregano (origanum vulgare, oil)
vitamin b2,Riboflavin
thyme (thymol, thyme oil)
nigella sativa seed (black cumin)
garlic (allium sativum)
foeniculum vulgare,fennel
rosmarinus officinalis,rosemary
green tea
Hesperidin (polyphenol)
vegetable/fruit juice-based diets
naringenin(grapefruit) (Flavonoid)
neem
lactobacillus kefiri (NOT KEFIR)
peppermint (spice, oil)
syzygium aromaticum (clove)
triphala

Looking at probiotics, we have a good number that would allow easy rotation of probiotics. Two are usually difficult to obtain: lactobacillus kefiri and lactobacillus sakei . Most are available at my usual two preferred sources: Custom Probiotics and Indian Bulk Exporter (Maple Life Sources). See this list for sources not available there. By rotation, I mean 20-50 BCFU daily of one probiotic for 2 weeks and then change to another probiotic.

lactobacillus kefiri (NOT KEFIR)
lactobacillus casei (probiotics) [CB,MLS]
lactobacillus sakei (probiotics)
lactobacillus salivarius (probiotics) [CB,MLS]
lactobacillus reuteri (probiotics) [CB,MLS]
bifidobacterium infantis,(probiotics) [CB,MLS]
enterococcus faecium (probiotic)
lactobacillus paracasei (probiotics) [CB,MLS]
clostridium butyricum (probiotics),Miya,Miyarisan

Items to Reduce or Avoid

The top items are below. In relationship to the take, it seems clear that spices and herbs may be critical — increasing vegetables may have limited benefit. Spices and herbs can be done as capsules, teas, oils or just putting on food.

Modifiers To Avoid
resistant starch
Slippery Elm
ß-glucan
arabinogalactan (prebiotic)
chestnut tannins
Pork
rice bran
aspartame (sweetner)
quercetin,resveratrol
navy bean
vitamin B3,niacin
high fiber diet
partially hydrolyzed guar gum
Bofutsushosan
Pumpkin
moderate-protein moderate-carbohydrate
resistant maltodextrin

The question of milk came up. AVOID . If you need a milk like substance, use Soy milk only – other milks will contain milk sugar.

  • Cow milk 4mg per 100ml
  • Goat milk 0.6mg per 100ml
  • Soy milk 0mg per 100ml

Bottom Line

This is an interesting sample, the very high number of high percentile bacteria (with corresponding low Eubiosis) present some challenges. The interesting thing is that just targeting the high percentile ones produce a similar set of suggestions as the “Just Give Me Suggestions”. The item that is interesting is the massive number of different herbs at the top of the list. With the Oral Bacteria leakage issue, strive to take them as teas.Caffeine is a weak to be avoided, so it looks like herb teas (without caffeine — i.e. not black teas with herbs, just pure herbs) will be the regular beverage.

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.

Example of how Lab Quality Can make Intrepretation Difficult + Oral Bacteria Issue

This person is a long time ME/CFSer. I should start by pointing out that the Eubiosis measure is easy to misinterpret. This person has a good 90.2% eubiosis. This indicates that things are more even (balance is likely a poor choice of word, too many meanings attached) — this is not a health measure as such. It’s a statistical measure whether the microbiome is matching the ideal pattern (not health specific).

Health Analysis is health orientated. Looking at those values we see a loss of health indicators while the evenness has improved.

  1. “Leaked” from Oral Cavity
    • By Taxa is 70%ile, was 48%ile (7/2023), 70% (09/2022)
    • By Volume 49%ile, was 19% (7/2023) , 38.5 (09/2022)
  2. Jason Criteria: 17%ile was 17%ile the same
  3. Key Symptoms bacteria went to 18 was 12

The Oral Cavity stands out as a concerning factor for this person.

Analysis

We have a historic trend of 6 samples. We need to be careful of our interpretation because of differences in Lab Read Quality. The Lab Read Quality bounces around, and with that, other values may echo these shifts (i.e. up to 20% shifts for some measures). A low read quality means less bacteria are reported, for example, when it was low, the Outside Kaltoft-Moldrup has low, when it was high, the value became high.

Another way to view it is this: If 10% are out of range and 850 are reported then we have 85. If we have 500 in another report then we would expect 50. This could be misread as a 85/50 or a 70% increase in out of range bacteria. Technically, it is more complicated but that should explain the problem.

We have only one item 🙂 that is a clear improvement and one item suggesting a loss :-(.

Criteria1/5/20247/3/20239/26/20221/9/20223/8/20217/26/2020
Eubiosis91.568.841.165.631.543.5
Lab Read Quality7.94.4113.33.63
Outside Range from GanzImmun Diagostics151519191313
Outside Range from JasonH445566
Outside Range from Lab Teletest212118182727
Outside Range from Medivere161617171313
Outside Range from Metagenomics557788
Outside Range from Microba Co-Biome222222
Outside Range from MyBioma10103399
Outside Range from Nirvana/CosmosId222218182020
Outside Range from Thorne (20/80%ile)215215224224228228
Outside Range from XenoGene363635353737
Outside Lab Range (+/- 1.96SD)7142101126
Outside Box-Plot-Whiskers5549467392103
Outside Kaltoft-Moldrup114 🙁7284473886
Bacteria Reported By Lab749545838495660483
Bacteria Over 90%ile23 🙂47346669100
Bacteria Under 10%ile49282111244
Shannon Diversity Index1.9581.1721.5951.4911.970.933
Simpson Diversity Index0.0410.2340.0750.1280.0450.012
Chao1 Index165547002186146127111127513
Pathogens322534292823
Condition Est. Over 90%ile000000
Actual Symptoms in top 10 Forecastedn/a5n/a358

We have a good number of bacteria strongly statistically associated with symptoms

The difference between the two symptom forecast methods is shown below. The newer method (genus only) appears to predict symptoms better

Going Forward

With the revised algorithm (see Algorithm for “Just Give Me Suggestions” with symptoms we get the following. Unlike many samples, there were few antibiotics at the top of the list.  

To Take

Spices and herbs can be done as capsules, teas, oils or just putting on food, but given the Oral leakage — as teas should be considered.

Modifier
whey
raffinose(sugar beet)
lactobacillus casei (probiotics)
fructo-oligosaccharides (prebiotic)
rosmarinus officinalis,rosemary
garlic (allium sativum)
lactobacillus paracasei (probiotics)
vitamin b2,Riboflavin
Lactobacillus Johnsonii (probiotic)
peppermint (spice, oil)
bifidobacterium longum bb536 (probiotics)
Cacao
trametes versicolor(Turkey tail mushroom)
lactobacillus reuteri (probiotics)
chondrus crispus,red sea weed
Dangshen
jerusalem artichoke (prebiotic)
lactobacillus sakei (probiotics)
lauric acid(fatty acid in coconut oil,in palm kernel oil,)
lactobacillus kefiri (NOT KEFIR)
green tea
foeniculum vulgare,fennel

Looking at probiotics, we have a good number that would allow easy rotation of probiotics. Two are usually difficult to obtain: lactobacillus kefiri and lactobacillus sakei . Most are available at my usual two preferred sources: Custom Probiotics and Indian Bulk Exporter (Maple Life Sources). See this list for sources not available there. By rotation, I mean 20-50 BCFU daily of one probiotic for 2 weeks and then change to another probiotic.

lactobacillus kefiri (NOT KEFIR)
lactobacillus casei (probiotics) [CB,MLS]
lactobacillus sakei (probiotics)
lactobacillus reuteri (probiotics) [CB,MLS]
bifidobacterium infantis,(probiotics) [CB,MLS]
bifidobacterium longum bb536 (probiotics)
lactobacillus paracasei (probiotics) [CB,MLS]
Lactobacillus Johnsonii [MLS]
Modifier To Avoid
saccharin
Ferric citrate (iron)
stevia
polydextrose
Pork
Slippery Elm
l-citrulline
nuts
Psyllium (Plantago Ovata Husk)
vegetarians Top of Form Bottom of Form
fibre-rich macrobiotic ma-pi 2 diet
Pulses
xylan (prebiotic)

Oral Bacteria Issue

This may be a likely contributor to ongoing issues. Why? the sinus and oral cavity repopulates the gut and undo prior improvements. My best suggestions are to address this are:

  • When possible, drink teas with the any of the suggested herbs.
  • Do not take probiotics as capsules, instead as powder dissolved in warm water and hold in the mouth before swallowing. See Symbioflor® 1 – Respiratory diseases | SymbioPharm, this may help.
  • Address any dental issues

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.

Key Bacteria Genus Associated to Patients Symptoms

This is a follow up to Technical Note: Identifying Key Bacteria to Address, part of this series Technical Notes on Microbiome Analysis. I am working with a new EU based start-up Precision Biome and in refining their algorithms they asked me to identify the key genus that should be considered (and other information).

The table below shows the top results that may be of interest in a clinical setting.

  • Occurrences is the number of times it was detected as statistically significant.
  • We averaged Chi2 to provide more generic detection.
  • [Shift] indicates if Chi2 is for the low range test or the high range test.
    • Low with High Count indicates that the absence of cells is more severe in the low range than than the abundance of cells in the top range.
    • Often there is a shift to upper, resulting in over population of the top range and almost complete disappearance of the low range.
  • Majority of the results were from 16s processing (with the inherent risk of misidentification)
  • Contrary to common belief, low levels seems to be rarely the apparent cause, they may be a consequence of multiple highs.
  • The data below can be replicated from data at https://citizenscience.microbiomeprescription.com/ (Open data) with the processes referred to above.
taxonTax NameShiftOccurrencesAverage Chi2Density
84567PedobacterLow355127.9High Count
114627AlkaliphilusLow356127.7High Count
33951AcetobacteriumLow358126.6High Count
190972SedimentibacterLow353126.4High Count
1769729HathewayaLow362126.4High Count
100883CoprobacillusLow360125.4High Count
28453SphingobacteriumLow350123High Count
970SelenomonasLow353120.1High Count
44000CaldicellulosiruptorLow352120High Count
1378GemellaLow353119.3High Count
82373AnaerovibrioLow350117.6High Count
281119Candidatus AmoebophilusLow352117.2High Count
29548RhodothermusLow348115.2High Count
69894TindalliaLow347110.1High Count
864PectinatusLow351108.1High Count
33926Candidatus PhytoplasmaLow340107.1High Count
256319ChlorobaculumLow348106.4High Count
89958NatronincolaLow332105.1High Count
2304693PseudoclostridiumLow346104.9High Count
561EscherichiaLow345103.6High Count
1647ErysipelothrixLow354103.6High Count
2093MycoplasmaLow345103.5High Count
46205PseudobutyrivibrioLow587103.4High Count
94008ThermicanusLow338103.2High Count
156973DysgonomonasLow345102.1High Count
119852OscillospiraLow569101.6High Count
1263RuminococcusLow669100.8High Count
2316020MediterraneibacterLow670100.7High Count
33042CoprococcusLow670100.5High Count
42447AnaerobrancaLow32899.7High Count
1350EnterococcusLow26499.3High Count
35829AcetivibrioLow66497.6High Count
1730EubacteriumLow66796.6High Count
44260MoorellaLow25496.3High Count
376469OlivibacterLow19896.1High Count
2740PeptococcusLow54395.2High Count
131079LimnobacterLow15195.2High Count
52784AnaerofilumLow52694.4High Count
44258CaloramatorLow62993.8High Count
572511BlautiaLow89793.3High Count
816BacteroidesLow89793.2High Count
841RoseburiaLow89793High Count
1485ClostridiumLow89692.8High Count
43994JohnsonellaLow61892.8High Count
265975OribacteriumLow66192.7High Count
216851FaecalibacteriumLow89792.7High Count
909656PhocaeicolaLow89592.6High Count
1301StreptococcusLow89492.4High Count
189330DoreaLow89792.4High Count
28050LachnospiraLow88492.3High Count
35832BilophilaLow55891.5High Count
375288ParabacteroidesLow88791.5High Count
906MegasphaeraLow55990.5High Count
140625LachnobacteriumLow63488.6High Count
1678BifidobacteriumLow86988High Count
244127AnaerotruncusLow86787.3High Count
207244AnaerostipesLow89386.4High Count
838PrevotellaLow85985.9High Count
40544SutterellaLow83985.2High Count
84108SlackiaLow50883.8High Count
29465VeillonellaLow84283.6High Count
1578LactobacillusLow87082.2High Count
162289PeptoniphilusLow85281.8High Count
283168OdoribacterLow85780.6High Count
61170HoldemaniaLow86079.5High Count
102106CollinsellaLow85379.3High Count
33024PhascolarctobacteriumLow85377.6High Count
447020AdlercreutziaLow47376.5High Count
1508657RuminiclostridiumLow43675.5High Count
724HaemophilusLow45174.5High Count
239934AkkermansiaLow82474.3High Count
86331MogibacteriumLow84173.5High Count
872DesulfovibrioLow80672.6High Count
836PorphyromonasLow81370.3High Count
84111EggerthellaLow76769.6High Count
574697ButyricimonasLow77969High Count
1266SarcinaLow22868.8High Count
1407607FusicatenibacterLow53568.2High Count
1506553LachnoclostridiumLow31468.1High Count
292632SubdoligranulumLow53768High Count
1505663ErysipelatoclostridiumLow54067.7High Count
1506577TyzzerellaLow31467.5High Count
577309ParaprevotellaLow41267.4High Count
946234FlavonifractorLow54067.3High Count
239759AlistipesLow54066.9High Count
1654ActinomycesLow71866.9High Count
43996CatonellaLow31266.5High Count
459786OscillibacterLow53766.3High Count
1769729HathewayaHigh27066.2High Count
1392389IntestinimonasLow53165.7High Count
84567PedobacterHigh26765.7High Count
1649459HungatellaLow31165.5High Count
33951AcetobacteriumHigh27065.5High Count
114627AlkaliphilusHigh27265.3High Count
1164882LachnoanaerobaculumLow31365.3High Count
2048137AgathobaculumLow31265.3High Count
698776CellulosilyticumLow30864.8High Count
2039240AnaerotignumLow31164.6High Count
100883CoprobacillusHigh27764.4High Count
190972SedimentibacterHigh26864.1High Count
52784AnaerofilumHigh29164High Count
2569097AnaerobutyricumLow30963.6High Count
1774128MurimonasLow30363.5High Count
2740PeptococcusHigh28263.4High Count
2719313EnteroclosterLow30963.3High Count
28453SphingobacteriumHigh26763.1High Count
970SelenomonasHigh25962.7High Count
1427378AcetatifactorLow30462.5High Count
44000CaldicellulosiruptorHigh25661.7High Count
1378GemellaHigh26961.4High Count
204475GemmigerLow30061.2High Count
119852OscillospiraHigh33361.1High Count
29548RhodothermusHigh25860.8High Count
281119Candidatus AmoebophilusHigh25360.5High Count
82373AnaerovibrioHigh25759.8High Count
1505657IntestinibacterLow48859.7High Count
248744MarvinbryantiaLow50259.4High Count
253238EthanoligenensLow30359.1High Count
46205PseudobutyrivibrioHigh37158.9High Count
241189HespelliaLow51958.3High Count
69894TindalliaHigh25257.7High Count
864PectinatusHigh25957.5High Count
89958NatronincolaHigh25357.4High Count
43994JohnsonellaHigh34657.4High Count
131079LimnobacterHigh14057.3High Count
1843210AnaerocolumnaLow29356.8High Count
44249PaenibacillusLow29756.7High Count
1481960PeptoclostridiumLow20856.7High Count
94008ThermicanusHigh25356.6High Count
84108SlackiaHigh27156.6High Count
577310ParasutterellaLow50156.5High Count
830ButyrivibrioLow49956.4High Count
906MegasphaeraHigh31556.4High Count
44258CaloramatorHigh35556.2High Count
256319ChlorobaculumHigh24756.1High Count
437755MoryellaLow49756.1High Count
1647ErysipelothrixHigh25556High Count
33926Candidatus PhytoplasmaHigh24456High Count
561EscherichiaHigh24755.9High Count
2304693PseudoclostridiumHigh24955.9High Count
33042CoprococcusHigh43855.5High Count
1505652TerrisporobacterLow50455.5High Count
1569SporosarcinaLow29455.5High Count
35829AcetivibrioHigh41055.3High Count
2316020MediterraneibacterHigh44155.2High Count
376469OlivibacterHigh18155.1High Count
2093MycoplasmaHigh25154.6High Count
588605RobinsoniellaLow29454.6High Count
156973DysgonomonasHigh25854.6High Count
35832BilophilaHigh31954.5High Count
1263RuminococcusHigh45654.5High Count
1562DesulfotomaculumLow28354.5High Count
838PrevotellaHigh44754.3High Count
140625LachnobacteriumHigh34854.1High Count
1350EnterococcusHigh22154.1High Count
44748SporobacterLow49354High Count
42447AnaerobrancaHigh24253.8High Count
40544SutterellaHigh44453.3High Count
162289PeptoniphilusHigh42853.1High Count
1485ClostridiumHigh53653High Count
909656PhocaeicolaHigh54152.9High Count
572511BlautiaHigh54552.8High Count
816BacteroidesHigh54852.8High Count
44260MoorellaHigh21252.6High Count
189330DoreaHigh54652.6High Count
841RoseburiaHigh55252.5High Count
1017280PseudoflavonifractorLow49052.4High Count
39948DialisterLow49852.3High Count
265975OribacteriumHigh41952.3High Count
216851FaecalibacteriumHigh56352.3High Count
1678BifidobacteriumHigh49252.1High Count
29465VeillonellaHigh45052.1High Count
66831FacklamiaLow27552High Count
244127AnaerotruncusHigh48052High Count
1730EubacteriumHigh46251.9High Count
375288ParabacteroidesHigh53951.9High Count
1301StreptococcusHigh56451.9High Count
28050LachnospiraHigh55551.6High Count
1501226RomboutsiaLow48051.3High Count
379899NiabellaLow29251.3High Count
1432051EisenbergiellaLow48550.5High Count
579KluyveraLow20850High Count
1578LactobacillusHigh47549.9High Count
283168OdoribacterHigh45649.6High Count
653683AnaerosporobacterLow20949.6High Count
724HaemophilusHigh26649.4High Count
207244AnaerostipesHigh54949.3High Count
61170HoldemaniaHigh44649.3High Count
404402HowardellaLow26849.2High Count
872DesulfovibrioHigh39548.7High Count
1433991BrassicibacterLow27048.6High Count
86331MogibacteriumHigh39648.6High Count
836PorphyromonasHigh39048.4High Count
33024PhascolarctobacteriumHigh43948.2High Count
1508657RuminiclostridiumHigh28548.1High Count
2282743DesulfohalotomaculumLow26947.9High Count
239934AkkermansiaHigh40747.7High Count
397864BarnesiellaLow47647.6High Count
447020AdlercreutziaHigh24747.3High Count
150022FinegoldiaLow48447.3High Count
1470353Candidatus SoleaferreaLow20147.1High Count
102106CollinsellaHigh47846.7High Count
577309ParaprevotellaHigh24346.4High Count
420345LactonifactorLow45146.3High Count
596767HydrogenoanaerobacteriumLow44145.8High Count
2529408SchaaliaLow20245.4High Count
574697ButyricimonasHigh38145High Count
1654ActinomycesHigh36145High Count
84111EggerthellaHigh39444.3High Count
177971ShuttleworthiaLow43442.5High Count
1870884ClostridioidesLow19342.5High Count
644652GordonibacterLow20041.7High Count
191303TuricibacterLow19041.6High Count
292632SubdoligranulumHigh25840.2High Count
1716CorynebacteriumLow20240High Count
1407607FusicatenibacterHigh26039.9High Count
946234FlavonifractorHigh25639.9High Count
459786OscillibacterHigh25139.8High Count
1392389IntestinimonasHigh24739.3High Count
1505663ErysipelatoclostridiumHigh27939.1High Count
1506577TyzzerellaHigh16139.1High Count
44748SporobacterHigh16338.5High Count
239759AlistipesHigh28338.4High Count
830ButyrivibrioHigh18138.2High Count
1164882LachnoanaerobaculumHigh15838.1High Count
43996CatonellaHigh16237.9High Count
1649459HungatellaHigh15537.9High Count
698776CellulosilyticumHigh15437.8High Count
241189HespelliaHigh20537.6High Count
2048137AgathobaculumHigh15137.4High Count
1774128MurimonasHigh14537.4High Count
100175PapillibacterLow19437.3High Count
2039240AnaerotignumHigh14837.3High Count
2569097AnaerobutyricumHigh14237.2High Count
1506553LachnoclostridiumHigh19137High Count
2719313EnteroclosterHigh14536.8High Count
596767HydrogenoanaerobacteriumHigh14836.8High Count
237FlavobacteriumLow16836.3High Count
1505657IntestinibacterHigh21036.3High Count
437755MoryellaHigh17436.2High Count
1427378AcetatifactorHigh14736.1High Count
577310ParasutterellaHigh19135.9High Count
253238EthanoligenensHigh13235.8High Count
165779AnaerococcusLow19435.7High Count
248744MarvinbryantiaHigh20435.4High Count
204475GemmigerHigh14534.9High Count
39948DialisterHigh16134.9High Count
397864BarnesiellaHigh12434.6High Count
420345LactonifactorHigh11534.5High Count
1017280PseudoflavonifractorHigh15734.4High Count
1505652TerrisporobacterHigh19034.2High Count
177971ShuttleworthiaHigh12034.2High Count
588605RobinsoniellaHigh11634High Count
1432051EisenbergiellaHigh16734High Count
1569SporosarcinaHigh12233.7High Count
44249PaenibacillusHigh12633.7High Count
1843210AnaerocolumnaHigh12833.6High Count
168934ThalassospiraLow17633.6High Count
1501226RomboutsiaHigh16533High Count
150022FinegoldiaHigh13032.8High Count
1562DesulfotomaculumHigh10932.6High Count
66831FacklamiaHigh10431.6High Count
1348911CoprobacterLow19431.4High Count
379899NiabellaHigh11031.3High Count
135858CatenibacteriumLow16928.9High Count
1472649DielmaLow18028High Count
117563GranulicatellaLow16226.3High Count
172900VictivallisLow15726.3High Count
194CampylobacterLow18126.1High Count
109326AnaerovoraxLow15525.7High Count
184869VaribaculumLow17824.7High Count
580024EnterorhabdusLow16724.5High Count
963HerbaspirillumLow15924.4High Count
1357LactococcusLow15723.8High Count
1161127MurdochiellaLow15422.2High Count
189326GelriaLow14920.7High Count
1473205SenegalimassiliaLow13520.4High Count
(c) 2024 Lassesen Consulting LLC, DBA Microbiome Prescription

Why are Metabolites different on same sample from different analysis?

A reader forward this image from BiomeSight to me:

Apart from wording being questionable (former technical writer speaking) because many people will read it as needing to be increased whereas the chart on the right clearly shows that it needs to be decreased.

Same sample on MP reports:

  • D-Lactic Acid 18%ile. Thus much lower than the mid point! A Contradiction! D-Lactic acid is the bad form of lactic acid. L-Lactic acid is the very good form!

A brief discussion of how metabolites are estimated. There are several approaches used by retail providers:

  • Based on clinical studies reporting that a certain bacteria produces this compound.
    • Then just total up the count of all such bacteria
  • Based on clinical studies reporting that a certain bacteria produces this compound AND the amount that each produces.
    • Then just total up the count times the amount of all such bacteria
  • Based on KEGG: Kyoto Encyclopedia of Genes and Genomes and derive the average amount per species (and/or genus)
    • Then just total up the count times the amount of all such bacteria
    • This is the method that Microbiome Prescription [MP] uses.

There are additional methods but most are significantly more expensive. Working from clinical studies always have the issue of some bacteria not being studies – hence estimates may be off.

Example of one metabolite (Reuterin) showing different amounts per bacteria according to strains

From prediction to function using evolutionary genomics: human-specific ecotypes of Lactobacillusreuteri have diverse probiotic functions[2014].

Bottom Line

There is no “right” answer. You should ask the provider of the estimates exactly how are metabolites computed (and data sources). In the case of MP, the source and method are clearly identified above. Additionally, the site should provide some education on the significance of each. Often metabolites are requested by customers and the provider does an “economical” analysis and implementation to satisfy the customer request; the results may be less than ideal or complete.

Often education is needed. The reader that emailed me, asked “should I not stop all lactate/lactic acid producing probiotics“. NO…. because L-Lactic acid is good and inhibits bad bacteria. So I checked L-Lactate (commonly just called Lactate) – see below.

Description on MP of this Metabolite

  1. D-Lactic Acidosis: Elevated levels of D-lactic acid in the blood can lead to a condition known as D-lactic acidosis. This occurs when the body’s ability to metabolize D-lactic acid is impaired or overwhelmed. It’s often associated with specific conditions such as short bowel syndrome (SBS) or other gastrointestinal disorders where there’s an increase in the production and absorption of D-lactic acid.
  2. Neurological Symptoms: D-lactic acidosis can lead to neurological symptoms, including confusion, impaired cognitive function, difficulty concentrating, and altered mental status. Severe cases may even lead to coma.
  3. Gastrointestinal Symptoms: Symptoms such as abdominal pain, diarrhea, and bloating can occur in individuals with D-lactic acidosis. These gastrointestinal symptoms are often related to the underlying conditions causing D-lactic acid accumulation.
  4. Metabolic Acidosis: Elevated D-lactic acid levels can contribute to metabolic acidosis, an imbalance in the body’s acid-base equilibrium, leading to a decrease in blood pH. This can have systemic effects and affect various organs and bodily functions.
  5. Impaired Energy Production: D-lactic acid can interfere with cellular metabolism and energy production, potentially contributing to fatigue and weakness.

Looking up Lactate Value

Clicking on this tab button shows the thousands of metabolites that can be estimated on MP from KEGG data which we can search over.

and we find Lactate (C3H6O3) listed at 27%. IMHO that is low and you want to increase it. The description provided on this is below.

  1. Energy Production: Lactate is produced as a result of the breakdown of glucose during anaerobic metabolism when the body’s demand for energy exceeds its oxygen supply. It serves as an alternative fuel source, particularly for muscles and red blood cells, and can be converted back into glucose (gluconeogenesis) in the liver.
  2. Exercise and Muscle Function: During intense physical activity, the body produces lactate as muscles work vigorously, leading to temporary increases in blood lactate levels. Contrary to earlier beliefs associating lactate with muscle fatigue and soreness, lactate is not the primary cause of muscle fatigue but is rather utilized as a fuel by muscles and other tissues.
  3. Lactate Threshold: The lactate threshold is the exercise intensity at which lactate begins to accumulate in the blood more rapidly than it can be cleared. Athletes often train to improve their lactate threshold, as it correlates with performance and endurance in certain sports.
  4. Clinical Implications: Elevated lactate levels in the blood (lactic acidosis) can occur due to various conditions, such as sepsis, shock, hypoxia, liver disease, certain medications, or metabolic disorders. Severe lactic acidosis can lead to symptoms such as rapid breathing, nausea, abdominal pain, and, in severe cases, it can be life-threatening if left untreated.
  5. Health Conditions: While lactate plays essential roles in energy metabolism, excessive accumulation due to underlying health conditions or imbalances can lead to health issues. Conditions associated with lactic acidosis require proper medical evaluation and treatment.
  6. Diagnostic Tool: Blood lactate levels are sometimes measured in clinical settings to assess tissue oxygenation, especially in emergency and critical care situations, as elevated lactate levels can indicate tissue hypoperfusion and metabolic stress.

2 year follow up: ME/CFS back to work

This is a follow up to this analysis ME/CFS after trying suggestions from Dr.A.I. from 2 years ago. The goal of MicrobiomePrescription is not to cure any condition — rather to generate suggestions that have a high probability of mitigate a person’s symptoms. Mitigate means reduce severity or eliminate. With some condition, it could result in a technical remission (i.e. no longer matches a diagnostic criteria). The term remission and not cure should be used always — because the microbiome could return to a dark place due to future events or inadequate ongoing care.

Update Story

I’ve been doing MUCH better for the last two years. I feel nowhere near the “normal” levels of energy that a 36 years old man should have and a lot of things are difficult, but I’ve been better and I’m able to work full time as a web developer, remotely. I know live with my significant other, and working + living with someone takes absolutely all of my energy, so I usually have no resources left to meet friends or do extra activities, but the fact of being able to work full time is a huge improvement compared to two years ago. Most of the brain fog has lifted. It comes back on my bad days, but it’s really not as bad as it used to be. 

I feel that my energy levels are going worse these days and it’s getting harder to work full time though. That’s why I’ve done another microbiome analysis, and it seems to be even “worse” than 2 years ago, according to Biomesight’s score. 

I still have trouble digesting things (even though it’s been a bit better the last two years, it has never been “normal” I think) and get diarrhea quite often. I usually have to go to the toilets 5-6 times a day. I’m still very skinny.

I take much less dietary supplements than I used to, but I’m still taking :

  • Acetyl L-Carnitine
  • Ubiquinole
  • R Lipoic Acid
  • B12
  • Vitamin D
  • Nattokinase

I’ve also done another round of “Spezzata”[Licorice] recently, but it definitely makes my blood pressure go up. I also eat a lot of dark chocolate and drink a lot of coffee.

My diet has changed a bit since I’ve started living with my Significant Other about a year ago. I eat a lot more rice than I used to now.

Analysis

The first thing that I noticed was the lab quality is down a lot. Lower quality means less bacteria types (793 dropped to 334) are identify and the estimated costs have greater uncertainty. On the plus side, all measures are the same or are significantly better.

CriteriaCurrent Sample
2024		Old Sample
2022
Lab Read Quality25.4
Lab Quality Adjustment Percentage85.9100
Outside Range from GanzImmun Diagostics1919
Outside Range from Lab Teletest2525
Outside Range from Medivere1515
Outside Range from Metagenomics99
Outside Range from Microba Co-Biome66
Outside Range from MyBioma88
Outside Range from Nirvana/CosmosId2121
Outside Range from Thorne (20/80%ile)327327
Outside Range from XenoGene4141
Outside Lab Range (+/- 1.96SD)710
Outside Box-Plot-Whiskers43118
Outside Kaltoft-Moldrup2468
Bacteria Reported By Lab334793
Bacteria Over 90%ile099
Bacteria Under 10%ile031
Lab: BiomeSight
Pathogens1641
Condition Est. Over 90%ile03
Standard Items

Looking at new features added. Note that the drop in number of bacteria reported impacts many of these values)

Measure20242022
“Leaked” from Oral Cavity [LOW is better]21.1%ile65.7%ile
General Health Predictors [More is better]617
Jason Hawrelak Ratio 10%ile14%ile
Butyrate9%ile29%ile
Potential Medical Conditions Detected03
Bacteria deemed Unhealthy031
Eubiosis8%71.6%ile

The charts show similar patterns but with a group of bacteria dominating (80-90%ile) range

Conclusion: He is better than 2022 in many measures but is worse in a few (especially newer ones).

Let us look at some recent feature additions. First key bacteria — we see improvement we a lot of key bacteria dropping down below the threshold. (see Technical Note: Identifying Key Bacteria to Address for background)

“Leaked” from Oral Cavity is based on this study Oral bacteria relative abundance in faeces increases due to gut microbiota depletion and is linked with patient outcomes, 2024. As with above, we see improvement.

  • 2024: 21.1 Percentile.
  • 2022: 65.7 Percentile

Going Forward

As usual, I start with “Just give me Suggestions include Symptoms” with the new refactored algorithm (see Algorithm for “Just Give Me Suggestions”). The items were similar but with just a change of order.

First, let us look at what is currently being take. Microbiome changes over time. The highest for non-prescription items is 327 and lowest -516.

  • Acetyl L-Carnitine: 152
  • Ubiquinole: AKA COq 10, Not on current suggestions
  • R Lipoic Acid: Not on current suggestions
  • B12: 82
  • Vitamin D: -152
  • Nattokinase: looking at bacillus subtilis natto -39
  • Spezzata [glycyrrhizic acid (licorice)]: -42
  • chocolate : 11.5
  • coffee/ Trigonelline (found in Coffee): 152

None of the above is clearly a bad choice. The worst, vitamin D tend to be a slow acting supplement. This illustrates that doing a retest every 6 months to reset your course to recovery is likely good practice.

Some observations on suggestions:

AVOID List

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.