Myalgic Encephalomyelitis Microbiome Analysis

Reminder:

I am a computer scientist and a statistician. I am not licensed to practice medicine, and where I live has strict laws about ‘appearing to practice medicine’. What I can do for readers is to write a public blog (anonymous) from your data and back story as an education post on using the software and the statistics it produces. I cannot consult. The content should be reviewed by a medical professional before implementing.

Video walkthru of this blog

Back Story

35yr old, female with ME of around 15 years, Coeliac and Crohn’s diagnosed in 2014 plus simple temporal lobe seizures and endometriosis.

I have tested extremely extensively and most labs are generally normal with the exception of:

  • Prolactin- always slightly above high end of range
  • Lyme ELISA IgM positive but Blot negative (possibly cross-reactive with RF)
  • Rheumatoid factor – one point over upper range
  • LDH – consistently slightly above range
  • Aldolase – tested once, slightly above range
  • ALT – occasionally slightly above range
  • EBV – positive for past infection but never any evidence of reactivation
  • SIBO breath test positive for hydrogen only

I am really struggling with acne… I have been offered Lymecycline for the acne but don’t know if it’s worth the risk. I am currently on a 7-day course of Co-amoxiclav (amoxicillin + clavulanic acid) for an infected cyst (my Biome sample was taken before this).

I was able to control my crohn’s with an elemental diet, followed by strict paleo, then gradually reverting to a more relaxed diet. I did a course of oregano oil which was very harsh on the gut but it got rid of my constant bloating for the first time in my life (this came back and remains since reintroducing carbs). I’m 99.9% sure I’m on the autism spectrum. Interestingly, some of my autistic traits and my ME symptoms abate somewhat for a short period at the beginning of a cold virus (the first couple of days while fever is present). I had a similar temporary reaction to Sulforaphane.

My ME started while I was working full time, following glandular fever in 2006. The onset was characterised by ‘tired but wired’ and rolling PEM, finding it almost impossible to fall asleep until it was nearly time to get up and a complete inability to get into deep sleep. I reduced my working hours gradually but eventually gave up work fully in 2008. Even when ‘healthy’ I never had normal stamina, muscle mass and was really ready for bed by the end of the work day.

Possibly coinciding with my gastrointestinal diagnoses and subsequent avoidance of gluten, my symptoms calmed a bit from the ‘acute’ years, and I began to sleep a little better and get brief symptom-free interludes while at rest. Now, prolonged activity above baseline will lead to a return of the PEM and ‘tired but wired’ symptoms (inability to switch off nonsensical chattering thoughts at night leading to insomnia, feeling hot with chills, feverish, sweats, tossing and turning all night. These symptoms stop on rising but leave me extremely brain fogged from the sleep deprivation, and then repeat the next night. I also experience myalgia, headaches, orthostatic intolerance and strong need to lay horizontal throughout the day. I wake with heavy puffy face and eyelids most days. I go through periods of extreme dry mouth, worse on waking despite always hydrating well.

Even in my symptom-free-at-rest periods, I still struggle to get to sleep some nights, although I keep a strict routine 10pm-10am. I find it very difficult to get into the deeper stages of sleep almost all of the time. Even with all reasonable interventions and ear plugs I am easily startled awake by household sounds and there is usually activity from others from 4-5am onwards.

Microbiome Analysis

I am going to do three levels of Analysis. I will start with generic, then move on to diagnosis using US National Library of Medicine studies and ending with the latest refactor, using bacteria associated with symptoms discovered from uploads to this site.
The purpose of these analysis to get suggestions for the most probable bacteria causing issues.

Overall Health

A domination of unhealthy bacteria
ME/CFS patients tend to have low blood pressure, do ignore hypertension. Acne and Insomnia are reported symptoms — so we have the microbiome matching the conditions. See Q&A for more information.

I will not go step by step (see this post with video for how to do this) but do the following suggestion generation and then look at the consensus

Then I went to Advance Suggestion with Percentile: 15% and the following PubMed conditions (Remember that Display Level must be Intermediate or higher to see this option):

  • Acne – 3 bacteria
  • Crohn’s Disease – 24 bacteria
  • Celiac Disease – 14 bacteria
  • Chronic Fatigue Syndrome – 13 bacteria

Then I went to Symptom Associated to Bacteria (Citizen Science) and found the following applicable items:

For Official Diagnosis: Chronic Fatigue Syndrome (CFS/ME), most of the matched were at the Genus Level

For Official Diagnosis: Chronic Fatigue Syndrome (CFS/ME), most of the matched were at the Genus Level. Most of the matches are usually at the species level.

The result is 40 bacteria added to our hand picked list.

Consensus Highlights

We have a lot of different suggestions over our 10 analysis, often more than 1000!

Suggestions to discuss with your medical professional

On the avoid list:

Also listed was gluten-free diet. I suspect the type of gluten may be significant.

KEGG Probiotics:

The usual one for ME/CFS are at the top (and were also listed in Safer or Safest Takes) :

For supplements:

  • beta-alanine – Percentile: 9.7
  • D-Ribose – Percentile: 4
  • Glycine – Percentile: 13.6
  • L-Cysteine – Percentile: 13.6
  • L-Threonine – Percentile: 6.5
  • Magnesium – Percentile: 0.1

Both D-Ribose and Magnesium are well studied supplements in a ME/CFS context (confirming predictions to clinical practice the items are linked to CFSRemission Blog).

Bottom Line

At this point I will stop for several reasons:

  • Purpose was to show the method
  • Person has brain fog often, so more notes may be counter productive
  • ME/CFS usually have restricted funds, so keeping the number of items low reduces frustrations over not being able to acquire.

A video will be added in the next few days

Questions And Answers

Q: I forgot to mention it, but I do have allergic rhinitis and high cholesterol (as listed under the detected conditions) so this is very accurate.

A: Although I see this often, it keeps surprising me about the accuracy of predictions!

Q: Interesting that it doesn’t pick up on any CFS-related bacteria at a species level, I wonder if this fluctuates and could possibly be because I was relatively low-symptom at the time of the sample, i.e. not in a PEM flare? 

A: You are very likely correct, it does fluctuates. Also, keep in mind that there are many subsets of ME/CFS, so this can be a little hit-and-miss.

Should I take Lymecycline?

A: This is a little complex, we have mixed results.

But when I tried a different antibiotic often prescribed for acne, it is all positive

And my favorite because it reduce inflammation and crosses the blood-brain barrier:

I would suggest making a counter proposal to your medical professional of minocycline instead.

Q: I’d be interested in your opinion on IgY hyperimmune egg powder supplements for targeting gut pathogens

A: There are many retail products like this. What I found are some vet studies[36 listed here]. I found a list of clinical studies here. My general impression is that it is favorable. There is one word of caution, it appears similar to transfer factor — i.e. the IgY may be targeted to specific bacteria/infections only. Hence, my advice would be to buy just one unit of it, if no response, change to a different brand when you finish it. Remember my motto: Rotate, rotate, rotate….

Long term Fibromyalgia with Psoriatic Arthritis

Reminder:

I am a computer scientist and a statistician. I am not licensed to practice medicine, and where I live has strict laws about ‘appearing to practice medicine’. What I can do for readers is to write a public blog (anonymous) from your data and back story as an education post on using the software and the statistics it produces. I cannot consult. The content should be reviewed by a medical professional before implementing.

Back Story

  • Male, 57, very high pain tolerance, little tolerance of irritation (itch, slivers, paper cuts, cold, drafts)
    • Diagnosed with Fibromyalgia at age 35
    • Proposed diagnosis of Psoriatic Arthritis last year
  • Psoriasis (or eczema since 10 yrs old). Usually cold hands and feet.
  • Depression most of my life. 
    • Currently abated by Bupropion, past included: Serzone, Gabapentin,Lyrica
  • Always loose bowel movements, but not diarrhea.  Never constipated.
  • Musculoskeletal pain all my life. Not worse with activity.
  • Restless leg syndrome while sitting,  Had to shift every thirty seconds. 
    • Took pamiprexole for 4 mos.  Stopped PPX, restless leg never returned.
  • Felt sick with Aspartame. (Phenylalanine)
  • About 20 years ago, with the intention of it being an elimination diet, lived on nothing but boiled eggs and (Chinese dish) Beef & Broccoli (with GF soy sauce, sesame oil, garlic, ginger and olive oil). Swallowed Tbsp of turmeric daily.
    • After 7 months, complete remission.
    • Lapsed diet, Remission lasted 4 mos.  Woke up one morning fully sick. 
  • Went on a gluten free, seed free, seed oil free, ketogenic diet about 10 years ago. I suspect the lack of carbs starved a Candida problem.  Much reduced symptoms for about 8 years, downhill slide the last two.
  • Taken arthritis-related herbs the last year.  Researching each, (about a hundred researched, perhaps 15 taken) they all seem to benefit the microbiome.
  • My kidney and liver labs are very good. My heart scan showed zero plaque deposits.
  • Life is pretty miserable.

Note on Fibromyalgia: Bacteria Associated from PubMed, Bacteria Associated from Citizen Science. The only bacteria in common with these two lists is: Hungatella hathewayi. IMHO, Fibromyalgia (as a diagnosis) by itself does not have a strong relationship to the microbiome. There may be strong associations of symptoms to the microbiome.

Microbiome Analysis

I am going to do three levels of Analysis. I will start with generic, then move on to diagnosis using US National Library of Medicine studies and ending with the latest refactor, using bacteria associated with symptoms discovered from uploads to this site.
The purpose of these analysis to get suggestions for the most probable bacteria causing issues

Generic Analysis – Pass #1

This is the suggested path for a first time user to take. We are not targeting for specific issues, rather trying to improve the microbiome towards a typical microbiome. For many people that is sufficient

With the large number of medical issues described above I started by looking at potential medical conditions using National Library of Medicine data. One of the challenges is that the microbiome profiles are often based on naïve patients (i.e. not being treated for anything), he is being treated.

Yellow items are significant risk [i.e. Percentile Greater than (100-prevalence/2) ]

Going further down the page, we see that your microbiome does not have major dysfunction by Dr. Hawrelak criteria (89%ile)

Jumping directly to suggestions

It was interesting that KEGG AI Computed probiotics was very similar to those from a sample that I did a video on [ miyarisan (jp) / miyarisan, enviromedica terraflora sbo probiotic, CustomProbiotics.com / L. Plantarum Probiotic Powder, symbiopharm / symbioflor 1]. For supplements, only L-Threonine – was suggested at a Percentile of 6.8%ile.

Expert Criteria with Consensus

I proceeded to the Expert Criteria page and did each option. I then use the consensus report to identify the best candidates.

The first ones (Use…) all just picked 8 bacteria. Standard Lab Ranges picked 12 bacteria, Box Plot: 55, Kaltoft-Moltrup : 73 and Top/Bottom at 10%: 70. As a reminder, the consensus button appears after doing two suggestions sets in 24 hours. An alternative (since the first 5 picked the same bacteria) is to do just one of the “Use” and each of the others, then look at the consensus (left as an exercise to the reader).

Consensus data is kept for 24 hours only, or when a user clear them

The consensus report key suggestions were:

I noted that some of his past diet types are on the Adverse Risk list, i.e. those choices may have contributed to where he is now (not immediate, but keeping to them long term).

National Library of Medicine Conditions – Pass #2

For this pass, we clear our consensus suggestion. We want the suggestions to be specific.

How to clear consensus suggestions so we can build a new set.
We then go to Advance Suggestions.

Since this person has been taking a variety of prescription drugs, I am including that in suggestions. The main reason is to see if there are alternative prescriptions possible that may be more microbiome beneficial. For ME/CFS, often the top items with this choice have been antibiotics that have been used successfully for treating ME/CFS (despite the AI not having that information).

First, we need to determine the conditions that we have data available for and that this reader has. I extracted these as candidates:

I picked the settings below for the first one. I checked ALL types of Bacteria Modifiers.

For each condition, I just change the last select box.

I will skip the avoid list, they should be reviewed by the reader. What is interesting to note was that both antihistamine and antifungal drugs showed up based on the bacteria patterns. This suggests that those two issues may warrant investigation.

P.S. I picked 15% arbitrarily, I like to shoot for an average of 6-10 bacteria per set of suggestions being selected to keep the suggestions focused. You may wish to increase or decrease to tune the number selected.

Using Symptoms – Pass #3

This comes out of this weeks refactor. A video of this feature is below (TO DO).

Again, clear the consensus as we did above. Why, because we will likely be running several list of suggestions.

Where this new feature landed (the name may change a little). Clicking on the link and then entering “Depression” will give you a few choices.
I went with the General Depression — sample size was bigger than the others, and thus the bacteria identified was more.

On the resulting page, you will see checkboxes to pick the bacteria that are likely good candidates to change. I went and checked all of them and then clicked the [Add to Hand Pick Selection] button at the top.

I then checked Fibromyalgia and had no luck (we have a small number of people with this condition, so detection is poor).

I then went on to pain, as shown below, and picked General: Myalgia (pain)

We now have a different list of bacteria

Again, I checked all of the available checkboxes and click to Hand Pick Selection. Then I went to Comorbid: Restless Leg which had only one bacteria with a checkbox.

At this point, I notice that a Hand Picked Bacteria button appears on my samples page

First view what was selected. We have a total of 8 bacteria, sufficient (I hope).

We then pick the suggestions link on the same drop down. Again pick all modifiers.

The list is similar to the early ones. Choline Deficiency means reduce choline intake.
The avoid list — many of the items were seen on the avoid lists above. For a few items we have disagreement, but for most, agreement.

For retail probiotics, we have long list with most having similar benefit

Note why the values are the same, many have nothing in common

Personally, I would likely drop these into rotation (there are no bacteria common to any of them):

  • wakamoto (jp) / wakamoto pharmaceutical intestinal drug
  •  customprobiotics.com / B. Bifidum Probiotic Powder
  •  shin biofermin (jp) /s
  •  optibac / saccharomyces boulardii

Bottom Line

Above we saw three different approaches to obtaining suggestions. There was agreement between each of the approaches for over 70% of the items. My usual suggestion to discuss with your MD before starting:

  • Take 2 of the following probiotics for two weeks and then rotate to a different pair
  • For foods and supplements
    • Niacin keeps appearing as a to take
    • Do NOT take a B-Complex, several of the B Vitamins are counterindicated
    • Barley (suggest for porridge on most days)
    • Inulin
    • For diet type — the reader needs to do a little work to decide what to do. Some of what he has tried are on the avoid list!

“I feel like I am hyper coagulated..”

Someone mentions that to me. My initial response is simple… don’t jump to conclusions without supporting lab results. Without lab results, you may feel the same from any of many condition that produces hypoxia (low oxygen delivery). Hyper-coagulation is one possible cause there are others. This is a quick list of items to get objective measures from..

  • First, get and monitor your saturated oxygen level. A lot of people have the Fingertip Pulse Oximeters. They are cheap and often under $20. With COVID persisting, they should be in every home first aid kit!
    • Both my wife and I wear a watch that records Saturated O2 every 15 minutes and we can view our history on our phone. See this post.
Fingertip Pulse Oximeter, Blood Oxygen Saturation Monitor (SpO2) with Pulse Rate Measurements and Pulse Bar Graph, Portable Digital Reading LED Display, Batteries and Carry Case Included

Bottom line: Get lab results when possible and do not speculate. I recall that some supplements will improve certain types of hypercoagulation and make other types worse. Act from objective knowledge and not speculation.

No description available.
Example of our family testing. This was done by Hemex, a specialized lab in coagulation. Any one of these can indicate hypercoagulation. Many physician will order only one or two items and them proclaim there is no evidence…

A reader experience with CFS and Autism

Sue, a reader in Australia, shared her experience below on the challenge of taking supplements. Other people may have the same challenge. In some cases, retail products additives can be the source of problems. In this house, we tend to make our own or use additive free.

The problem began when Ken Lassesen’s brilliant AI came up with oils my daughter must take by swallowing them, with high probability of success. Coriander, thyme, lavender, perilla oils. She’s been sick to the point of house-bound for years, and we’ve got to get her into life. She has autism and chronic fatigue, and since 2018  Ken Lassesen’s AI  has at least got her out of bed (unexpectedly, skads of licorice and thyme leaves are  key players here) when no kindly, well-informed, hard-working doctor could achieve that.

So- where to get the oils? First call was to my excellent local pharmacy in Sydney – Newton’s – and they told me that their oils shouldn’t be ingested, but they’d heard of a place “somewhere in NSW” called “something like” TERRA,  and they were “a bit expensive”. I found and rang TERRA, and they sent me the oils, one expensive from a company that’s licensed to provide ingestible oils, the other from a second company that I was assured was as good but hasn’t gone through the rigours of getting a license.

Now, how to get them into her. We tried dripping it into Bonvit gel caps  from our local chemist with some “blotting paper” in the bottom of thiamine which she has to take anyway, but they disintegrated almost as we looked at them. Bonvit are  fine with powders, but oils aren’t powders! Then we tried Surgipack’s capsules which were sturdier so they  lasted until she put them in her mouth. A few seconds later, howls of pain.  

Next morning we thought we had the solution and tracked down two sizes of Surgipack, so we put the oil and thiamine mixture into the smaller one and put that inside the bigger one, carefully wiping down the outside surface. We were very pleased with ourselves until a phone call with howls of pain with a burning oesophagus and stomach. I talked her into trying to take them right in the middle of breakfast, and she agreed to give them another go. It was still painful afterwards but she bravely soldiered on, saying that “it might be working” !  But after five days, the pain got too much to bear and she said she’d  “never have that stuff again. However good it’s supposed to be”.

But there must be nasty meds taken all the time, so how do the commercial companies get them into people without the whole nation howling in pain, with mass revolts? They must know something we don’t. 

We have a lot of private compounding chemists here so I rang around and asked them, one after another, if they used special capsules and could I buy some. But they make their money out of compounding, not selling their ingredients, so no. At last I chanced on a chatty girl who said what I needed was enteric-coated capsules”, but that her company couldn’t supply them. She vaguely mentioned legal reasons.

So then, the internet. We immediately found a supplier of enteric capsules in Australia, The Capsule Guy, costing $17 for 250 capsules. They come in sizes and we chose smallish ones, so we could put them inside a larger Surgipack capsule in case of dribbles.

We began 4 days ago. No howls. Then joy.  Yesterday afternoon, her birthday, she went out to the party of a childhood friend who has the same birthday. She only stayed 3 hours before she wilted, but she went out and we are over the moon. Thank you, Ken. You are bringing our daughter into life.

Post-Script

Reading an account like this makes all of the hours that I spent on the blog and web site worthwhile. Thank you Sue for sharing! P.S. Sue started in 2018, it is not an overnight turnaround, it is a slow long march. Each person is unique, as is their microbiome. Microbiome Prescription is specific to an individual’s microbiome and not their diagnosis.

Distribution of Jason Hawrelak Criteria

I offer Jason Hawrelak Criteria on my health page on Microbiome Prescription as shown below.

There are 15 Criteria

Doing the refactor, audit and re-validation of the site, a reader asked about their percentile ranking against the above. Good question and relatively easy to answer.

Percent of Healthy MatchesCountSamplesCommutive Percentile
00391.5%
6.71694%
13.321339%
20326619%
26.7443935.4%
33.3556456.5%
40650475.3%
46.7736589%
53.3817895.6%
6098598.8
66.7102499.7%
73.311499.9
80124100%

Bottom line is simple, if you have 40% (6 items) healthy – you are better than typical person. I would not be concerned about trying to raise it higher…. Not a single person has made it over 80% of the criteria….

Plotting the data revealed a logistic curve, which seems to constantly occur with microbiome data.

Revised Possible Medical Conditions Detected

A post on Facebook reminded me of an update from a recent data addition. We have added the prevalence of each condition. If you are at 75% ile for a condition that impacts only 5% of the population — there is low risk. But if the conditions impacts 50% of the population, you are at a significant risk.

Old display = items were picked on being outside of KM ranges.
The revised version … COVID-19 above suggests increased severity risk

Actions?

First, you should inform your medical professional that you are concerned about elevated risk for conditions that you do not have and inquire about any testing. Do not be surprised at some “rolling of the eyes” on how this risk was determined. Remember — many of the drugs prescribed for conditions do alter your microbiome in a favorable way (academic question: is this a possible mechanism of action?)

Second, for items of the greatest concern, you may wish filter by the bacteria associated with this condition to get suggestions that may shift your microbiome away from this profile.

Change Display Level to intermediate or higher to expose Advance Suggestions

Click on that link and then

Pick the condition that you are concerned about…

You may wish to play around with different filtering criteria

Microbiome Data is FUZZY not fixed

One reader keep coming back to me wanting definitive comprehensive answers. There is no such thing.

Let us walk thru all of the layers of randomness..

  • Your stool sample will vary according to time of day. The bacteria will change according to the last meal and the time since the last meal.
  • Where you sample your stool (outside, inside, front, back) will have different bacteria
  • The amount/quality of your sample will vary. uBiome did an informative: Count and then Count_norm
    • Count_norm is the count scaled to out of one million
    • Count is actual detected count… I have see that vary between 80,000 and 800,000
  • There is differences between the machines used (different primers etc) by the lab
  • The raw data file, FASTQ, (like a personal DNA sample) is interpreted by software.
    • If you have done your personal DNA, various sites will interpret what your ethnic inheritance is. The same applies to the software used to read the FASTQ file. See example below
    • Ombre and BiomeSight uses the same lab service but different software (in fact, Biomesight gives an option of a third software for interpretation.
  • Labs software disagrees about amount of each type of bacteria and even which ones are reported!
  • When we apply KEGG data, we have two randomness:
    • Does KEGG have data on the bacteria reported…. for some yes, at the strain level. We estimate genus level from strains… these are rough estimates and not necessarily accurate
    • Does the Lab report on those bacteria. In some cases yes, in other cases no.
  • Percentiles are based on the uploads. There is no question that there will be some bias in the samples, thus percentiles are reasonable but not accurate. When the number of samples with a specific bacteria is less than 200, then the percentiles reported may be easily off by 5-10%ile. This is due to the small sample size.
My DNA from Ancestry
My DNA from 23AndMe

Bottom Line

I understand that people want definitive, cast in bronze, answers. What is available is a fuzzy answer. IMHO, a fuzzy answer is far better than no answer or an answer by random reading of a posting on the web.

I describe the suggestions coming off Microbiome Prescription as being more lively to make the desired changes than trying random items or items suggested by web-self-reporting experience. It is like the stock market, AI can suggest stocks that are more likely to go up than down in purchase value. Buying gold or putting money under your mattress is also subject to changes in purchase value. Life is a random number generator, when you understand that, you can make better choices once you have done your homework.

Refactor “Changing Your Microbiome”

Often I am faced with requests to keep things simpler of the Microbiome Prescription site while getting requests to give more choices (often arising from people’s belief of what may work). I have just finished a revision attempting to balance these two (and set up infrastructure to give more choices in the future)

Old version menu of choices – with intermediate display
Revised version menu of choices – with intermediate display

The Expert Criteria takes you to a new page that has many criteria listed:

Expert Criteria Choices (more may be added as data becomes available)

There will be differences from each choice, because the bacteria selected will likely be different. For one sample:

  •  Use JasonH (15 Criteria) – 7 bacteria
  •  Use Medivere (54 Criteria) – 7 bacteria
  •  Use Metagenomics (59 Criteria) – 7 Bacteria
  •  Use Nirvana/CosmosId (36 Criteria) – 7 Bacteria
  •  Use XenoGene (22 Criteria) – 7 Bacteria
  •  Standard Lab Ranges (+/- 2 Std Dev) – 9 Bacteria
  •  Box Plot Whisker – 59 Bacteria
  •  Kaltoft-Moltrup Normal Ranges – 64 Bacteria
  •  Percentile in top or bottom %
    • 10% — 127 Bacteria
    • 5% — 55 Bacteria
    • 1% — 6 Bacteria

Why the differences? With only a few dozen bacteria with ranges, the chance of being picked is low. Box Plot and KM are computed for almost every bacteria. So with 700 bacteria, we have around 10% picked. With just 50 bacteria to be examined, we have around 14% picked.

These choices are also available in Advance Suggestions

What I do for gut health…

On facebook, I was asked:

Can you guys tell us beginners what do you guys do for gut health

If in unhealth…

My approach is simple, get a 16s (Biomesight or Ombre) microbiome test. Transfer or upload the data to https://microbiomeprescription.com/, get suggestions and do them for 4-8 weeks. Retest and repeat.

Here is an example of my applying this method (with 8 blog posts)

A key item is to rotate, rotate, rotate. Take the list of take suggestions and break into 4 groups. Do each for 2 weeks and then change to the next group. Attempt to remove ALL of the avoids (at least those with a value of 0.4 and higher). Simple enough? (Apart from the methodology to select the bacteria to alter — a new video on methodology is in progress)

If in health

Every 6-9 months, My approach is simple, get a 16s (Biomesight or Ombre) microbiome test. Transfer or upload the data to https://microbiomeprescription.com/, get suggestions. Look at rotating in (2 weeks on, 4 weeks off) any items over 0.8 on the take. Try to reduce any items on the avoid over 0.4.

If I am prescribe an ongoing medicine, then I will take a sample after 4 weeks and make modifications to counter any adverse effects. If the medication is in the existing database, I would check if there is an excessive shift (in terms of percentile) of the bacteria that it is known to shift.

For items like vaccinations and short term antibiotics, I will wait at least 8 weeks, preferred 12 weeks, to allow my immune system to settle down.

Bottom Line

That’s it. I do not do items exclusively from suggestions. I may take other items for diverse reasons — if they are not high in the avoid list, I just keep taking them.

Q&A

Q: Do you drink Kefir in general for gut health?

A: No, unpredictability of which bacteria are in it. I tend to keep to researched strains only. For yogurt: Activa is an example, or Yakurt probiotic drink. Custom Probiotics is a regular source.

Calculating Bacteria to Bacteria Associations

This is a note for software engineers out there.

I have moved on to rework the existing code. The processing is done on a dedicated server (32GB of memory, SSD drives for SQL Server. A little over 15,700,000 combinations of taxon needs to be made. Each combination needs to get all data on these taxons that are concurrent in any samples.

  • I.e. All samples that have Taxon 123 and Taxon 432 being reported.
The CPU Specification
Task Manager during the run
The Data Server Specifications

The computations are done using Parallel and Concurrent libraries. All indices have been tuned for this analysis. The SQL Server and the utility to calculate the associations are on the same server – so no latency or network impact.

I found that the CPU temperatures exceed the maximum recommended for the CPU chip.

Original Run load. The load was throttled to 85-90% to keep the temperatures lower. The log of the run is below. Elapsed time 50 hours with the computer running at 98%. This excludes time to calculate the monotonic transformation of the data (the association is neither linear nor Bayesian). 
2022-03-27 20:12:08 Bacteria2Bacteria - 15,717,260 Items to Inspect
2022-03-29 22:48:34 Bacteria2Bacteria - 15,717,260 Items Inspected
2022-03-29 22:48:47 805,770 Items found

Bottom Line

This analysis likely qualifies for the “big data” label. So why is it worth it? The answer is simple, for some bacteria we have no information on what increases or decreases it. If we know which bacteria is associated with the bacteria growth or reduction, then we can synthesize modifiers of these bacteria that we lack information on.

This has not been implemented in suggestions (and will likely be available at the nerd level when it is).