“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).

Pending User Interface Changes

This year I have been focusing on a deep review of the code to improve accuracy and to address a variety of issues. The first item was redoing all of the KEGG Derived data (deriving compounds and enzymes at the species level instead of random strains). See KEGG Data being updated

The second item was cleaning up percentile computations on samples for:

  • Taxonomy
  • End Products
  • Compound Produced (KEGG)
  • Compound Consumed (KEGG)
  • Net Compound (Produced – Consumed) (KEGG)
  • Enzymes (KEGG)
  • Medical Conditions (US National Library of Medicine)

Combined with this was also implementing Display Levels across menu. See Display Levels.

Existing Menu Items

Original (overwhelming) menu

New Menu Items

Display Level: Public

Display Level: Beginner

Display Level: Intermediate

Display Level: Advance

Outliers Improved

In the earlier version, outliers and full data was on two separate pages. These has been combined into a single page with more options.

Are your abnormal?

Calculations are done for you to indicate the level where values may be out of range by random chance. This is illustrated below.

Display Level: Public — there are no options, top and bottom 5% is predefined
Example of clear evidence of microbiome issues. It looks like the production of Bacteriocins (natural antibiotics) is low, as well as low bile and butyrate production.
Display Level: Beginner – The Kaltoft-Moltrup ranges are an available filter
Display Level: Intermediate – Custom Percentiles ranges are an available filter
Display Level: Advance- All values is an available filter (this can also be done by setting Custom Percentile to 50%)

Bottom Line

I am hoping to have testing completed by the end of March and will then deploy

Comparing Probiotics using KEGG Data

While there is some research of probiotics (a little, tiny amount may be more accurate for most) with just 38 strains being researched and available for retail sale. While it is a known issue (with no enforcement) for the bacteria species in many probiotics being misidentified (see Deceptive Probiotic Labels or Assessment of commercial probiotic bacterial contents and label accuracy), for the page cited below, we will assume that they are accurate.

Fortunately due to the data on KEGG: Kyoto Encyclopedia of Genes and Genomes we know what products that most species produces, and can infer the quantity of these products/enzymes that are produced.

Emoji codes
  • 🍼 Probiotics
  • 🏭 Compound Produced – Factories
  • 🛍️ Compound Consumed (substrate) – Shopping basket
  • 🏗️ Enzymes- Constructs process
  • 🦠 Bacteria (general)
  • ⚖️ Compare items

Location of Pages

After login, change display Level (top left corner) to a higher level, you will see a new menu item appear with several new pages. This post focuses on the probiotic only.

Each page follows the same pattern. Compound listed on left, estimate of number of units produces by cell and alternative names. The Compound or Enzyme is link to the KEGG page providing more (usually very technical) information.

You can search by just typing the name in the search box. Some examples:

Does Probiotic-3 produce Hydrogen Sulfide?
Does Probiotic-3 generate histidine (which is then converted to histamine)
Does Probiotic-3 produce D-Lactic Acid (which is associated with brain fog)

Fast identification of Probiotics for specific purpose

This page shows the compound with links to lists of probiotics. On the far right is the ID from the Organic Acts Tests (OATS – where a match could be identified)

From MicrobiomePrescription : Probiotics to Change KEGG Compounds

An example of the linked to KEGG page is shown below. This page can be a good starting point for a long and steep learning curve.

Compare Probiotics Pages

These pages allows you to select two different probiotics and see what each produces.

Bottom Line

This provides information that bridges the gaps in published research. If you know what you are trying to increase or decrease, this should provide guidance for you to discuss with your medical professional.

Direct Links