Recent Updates Page 20

Unknown's avatar lassesen 2:17 pm on December 3, 2022  

Update on the best diet for an individual

I have update my 2018 post, on my MicrobiomePrescription site and I have also done a video on it.

Unknown's avatar lassesen 5:36 am on October 23, 2022  

Alcohol Intolerance in ME/CFS – A Model

While working on a different blog post on brain fog, the light went on for a model that may explain newly developed alcohol intolerance in ME/CFS. People tolerated and enjoyed alcohol before ME/CFS so the cause is not DNA for these people, but some change caused by ME/CFS.

A major subset of people with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) has excessive lactic acid, typically d-lactic acid, especially with cognitive issues (see Systematic review and meta-analysis of cognitive impairment in myalgic encephalomyelitis / chronic fatigue syndrome (ME/CFS). [2022])

What would consuming alcohol (known as ethanol) do to such a person? The answer is clear from the literature:

So the model is simple:

High Lactic Acid + alcohol => severe lactic acidosis

So the key issue is to reduce lactic acid levels. I have written about this many times over the years, a few examples:

Bottom Line

As a FYI, a few people using their microbiome results and my analysis site, Microbiome Prescription, has reported the ability to enjoy a glass of wine when they were intolerant before. There is hope.

Unknown's avatar lassesen 1:51 pm on October 18, 2022  

ME/CFS Treatment Suggestions

The following is suggested reading, https://shop.healthmasters.com.au/pages/chronic-fatigue-syndrome-cfs-treatment-recommendations

It gives an extensive list of suggestions with dosages and the studies they are based on, for example

It is a “all on-one-page” that is ideal to discuss with your medical professional.

WARNING ON LIFE STYLE SECTION

There are many nuisances in the studies cited that are missed or have misleading inferences. Simple example, “individuals who regularly exercised…. experience less fatigue”… could be restated as “individuals who experience less fatigue…. regularly exercised”. Causality is not in the evidence.

Also, Cognitive-behavioral therapy trials has many more than the single study cited — the majority of studies found that it did not help, or made people worse.

Unknown's avatar lassesen 4:41 am on October 10, 2022  

Simplified Suggestions for Microbiome Adjustments

For the last few months I have been working with someone that runs a Long COVID support group. This has resulted in more modifiers being added. One of the outcomes has just been added to the site. She requested that a simplified set of suggestions be added to the site to make her life easier. This consists of items she picked from her experience dealing with the group.

Where to transcribe or upload data (depending on which test)

16s High Resolution tests

These simplified suggestions has been added everywhere (tell me if I missed a page). If you use GI Map or similar reports, it is available after you have transferred and return to adjust suggestions. You should see these options on most suggestion pages now. To get this new condensed report, just click the checkbox.

Common Elements

GI Map and similar

The report is a CDV file (loads into Excel or other spreadsheet programs)

After loading, into Excel, you will need to adjust column widths

First Load
After re-formatting as a table

If an item is a Take, then a clinical dosage is given (if known). Clinical Dosages are those reported from studies listed on the U.S. National Library of Medicine Clinical Trials site.

Example from a 16s Sample

Other sections are shown below.

CAUTIONS

At the bottom of the page are some essential reminders.

Some of the clinical dosages above may be problematic with some medical conditions.

Dosages should be reviewed by a medical professional before starting.

The suggestions are based on a mathematical model. dosages are from clinical studies.

Unknown's avatar lassesen 7:25 pm on September 26, 2022  

ME/CFS Microbiome after 5 years

This is a follow up for a reader from 2017 (yes FIVE YEARS ago). It was when I was attempting to work suggestions by hand, before I handed that process to Dr. Artificial Intelligence.

Reader Back Story

I have not taken any probiotics for over 1 year. My medical treatment is pharmacological for type 2 diabetes, levothyroxine, hydroaltesone[Hydrocortisone], hydroferol[vitamin D3 analog] 1 a month, statins, Omega 3 and fenofibrate, I have not taken probiotics.

Symptoms persist, abdominal bloating, tiredness, unrefreshing sleep, PEM, sore throat, lack of energy, exercise intolerance, visión changes, all symptoms of ME/CFS

Also the increase un body weight has been considerable and it is not possible for me to lose weight, my complexion was thin.

The latest sample was from BiomeSight so the number comparison below is more out of interest than being a truly valid comparison (which would be same lab to same lab). On the surface of the comparison we see what appears to be significant improvement on high percentile bacteria but an increase of low percentile bacteria.

Using the various canned criteria (Jason H, Medivere, Metagenomics, MyBioma, and XenoGene), there has been no change. By “canned”, we mean the bacteria picked by various sources that are important –usually at the genus or family level. The criteria below these lines are sensitive to the lab and the quality of the sample.

CriteriaCurrent SampleOld Sample
Lab Read Quality6.98.4
Bacteria Reported By Lab543203
Bacteria Over 99%ile122
Bacteria Over 95%ile1040
Bacteria Over 90%ile2651
Bacteria Under 10%ile26231
Bacteria Under 5%ile20518
Bacteria Under 1%ile1472
Different Labs – Items Skipped
Pathogens3818
Outside Range from JasonH88
Outside Range from Medivere1313
Outside Range from Metagenomics1010
Outside Range from MyBioma99
Outside Range from Nirvana/CosmosId1313
Outside Range from XenoGene55
Outside Lab Range (+/- 1.96SD)920
Outside Box-Plot-Whiskers6147
Outside Kaltoft-Moldrup23689

Comparing Samples (limited)

In the old analysis I was using ratios to mean. I have since moved on to percentiles. The table below looks at the top items and compare to percentiles. Note: there can be differences between labs on what they called bacteria (see The taxonomy nightmare before Christmas… (2019)).

Bacteria (Ratio to mean)Old Sample
Ubiome		New Sample
Biomesight
Parasutterella: (14.2x)99.8%ileNot Reported
Sutterella99.7%ile95%ile
Adlercreutzia:  (6.84x)99%ile0%ile
Bilophila:  (6.36x)99%ile88%ile
Butyricimonas: (5.28x)99%ile40%ile
Oscillibacter: (3.69x)94%ileNot Reported
Intestinimonas: (3.36x)97%ileNot Reported
Odoribacter: (3.20x)97%ile40%ile
Flavonifractor: (3.1x)99%ileNot Reported
Parabacteroides distasonis88%ile97%ile
Bacteroides ovatus36%ile98%ile
Phocaeicola massiliensis95%ile99%
In general, there has been little significant change on the extreme bacteria between the labs

Going Forward

We are doing suggestions from the following:

The goal of doing consensus are two fold:

  • Identify items that will help all issues, instead of helping one and making another worst
  • Doing what is called Monte Carlo simulation to have more confidence because the data we are dealing with is fuzzy

As a FYI, the PubMed are done via the Research Features / Advance Suggestions. Some produced no suggestions (for example Diabetes — which may be due to the diabetes drugs normalizing the bacteria)

Top Items From Consensus

postubiome_consensusDownload

The top items (in descending order) are below. Unusually, every single one was a take recommendation for each set of suggestions generated above. There is a rather clear theme on fibers.

Probiotics

The top suggestions are below in decreasing order.

I noticed that both lactobacillus plantarum (probiotics) and bifidobacterium longum (probiotics) are in the list, as it was for the ME/CFS person in this post: An email from a ME/CFS reader on Probiotics. As with that person, symbioflor 2 e.coli probiotics (US Source, World Wide Source) is lower down on the list. I checked the KEGG AI Suggested Probiotics [revised], and got a low 4.9 for Escherichia coli (with the highest value being just a 7 – indicating reasonably good balance). Using uBiome data, Escherichia coli was the top choice with a big 108.1. I would be inclined to offer the same advance as I did with the email, “because this probiotic is known to persists, use one bottle as part of probiotic rotation” – even just taking once a week is fine.

REMEMBER: The order does not reflect effectiveness — it reflects the amount of research available, hence the term Confidence.

Avoid Items

We have a variety of items listed that are usually suggested for ME/CFS. The reason that they are suggested is that blood tests show low levels. I am becoming inclined to suspect that the low levels in the blood is because of greedy bad bacteria in the microbiome that consumes them before it get to the blood. SPECULATION: Taking them as a supplement, feeds the bad bacteria and keeps ME/CFS going.

Vitamin B injections are likely fine, probably good! “ Patients with myalgic encephalomyelitis (ME, also called chronic fatigue syndrome) may respond most favorably to frequent vitamin B12 injections” [2015]

The thing that I have noticed with analysis is that two people have the same diagnosis and common symptoms, but their microbiomes are different and the AI generated suggestions are very different.

Bottom Line

With no active work on the microbiome, the microbiome stayed similar. Some of the changes may be due to the drugs being used;  fenofibrate,(prescription) – reduces Odoribacter, Bilophila, Flavonifractor and Butyricicoccus (which we saw above)

I would suggest trying the above suggestions (after it is reviewed by your MD), and retest every 4 months. Looking at A History of Several 16s Tests and Suggestions which was done on another ME/CFS person, we saw improvements in the he various canned criteria (Jason H, Medivere, Metagenomics, MyBioma, and XenoGene) after 3-4 months.