Recent Updates

lassesen 4:29 pm on June 12, 2019  

Quick start to 2 blogs and an analysis site

My primary concern for the last 20 years was been the condition known as Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). I deduced some seven+ years ago that the simplest explanation of the multitude of symptoms and abnormalities reported was a stable microbiome dysfunction. This explanation can also be applied to many other conditions. My focus is still on ME/CFS but I wish to make the data and algorithms available to people with any conditions. My old home page is here (dry technical).

The basic model that is supported by studies is:

  • DNA Snps that results in increased risk
  • Environmental changes of DNA (epigenetics) that further increase risk
  • Microbiome function that acts as a catalyst to the risk.

The microbiome is the simplest to alter technically — but very complex to alter because there are thousands of bacteria that interact with each other in the human body. DNA can also encourage some bacteria and discourage others. Example: Typhoid Mary is an excellent example of some one whose DNA and a nasty bacterial infection co-existed nicely.

Does changing the microbiome work for ME/CFS?

Answer is yes:

Open-label pilot for treatment targeting gut dysbiosis in myalgic encephalomyelitis/chronic fatigue syndrome: neuropsychological symptoms and sex comparisons , 2018
Ep. 49 Interview Ken Lassesen: Using AI to Improve the Gut Microbiome

Recommended Site For Testing

With ME/CFS, there is always a nasty cost factor for testing. My usual recommendation is for the cheapest, high quality provider that provides information for upload to my analysis site. Some sites provide a mountain more of information — but the benefit from that extra information is almost nothing (and it adds $$$$ and complexity).

  • uBiome.com is shutting down. This had been my personal usual site because using a variety of techniques, the cost was $25/sample. Don’t order from there.
  • Thryve is what I am starting to use. Their reports may be processed here for independent suggestions. I would also recommend

Who am I?

I am a citizen-scientist with reasonable scientist credentials: taught Chemistry and Physics at College Level; Master of Science, accepted for the PhD program, certified data scientist with R, one of the top mathematics and physics competition students in Canada during my university years, etc.

I am a closet academic — so I give links to my source of information everywhere and usually keep them to the highest quality sources (PubMed, professional journals). I have even had a letter of mine published in the Lancet.

The Sites

  • This site — over 1200 blog posts published over the last 5 years. This is where I publish most. You can subscribe to get new posts by email.
  • Microbiome Prescription site – started in 2018. This is a massive data store with a variety of artificial intelligence algorithms applied to it. Almost 800 people have uploaded their microbiome results to it and many annotated it with their symptoms.
  • Microbiome Prescription Word Press – started recently. This is intended as a reference to the above site. Just essential pages and a bunch of homemade videos taking you through some features.
  • Facebook Site: Where I usually post new blog entries and the occasional odd note that is not worth a blog post. Make sure that you like it so you get notices of new posts.

Findings to Date

The assumption that bacteria shifts connect to symptoms appears confirmed using the upload microbiomes.

  • We have found statistically significant patterns of some bacteria to symptoms, see this post
  • We appear to have a high probability of correctly predicting symptoms from a microbiome report. See this post.

These findings can be independently confirmed by using the public shared data at: http://lassesen.com/ubiome/

Tools to Help

The Microbiome Prescription site is a theoretical site, that is, it works from the logical application of data and is not based on actual human experience. It does have the ability to create suggestions of things to take and to avoid to try reducing abnormalities in your microbiome. It supports multiple models and algorithms because we do not know which actually works best.

The site states that the suggestions should be reviewed by a medical professional. The source of the information is provided by links (hundreds of articles are cited).

Evolving Story

As more data comes in, and more insight happens, there will be more posts and more features (some labelled experimental — because I am unsure of their accuracy) will be added. This is citizen science.

Video to kickstart using your microbiome use

lassesen 4:19 pm on March 18, 2020  

Post Viral Syndrome – Case Study

On Feb 15th I was running a high temperature, definitely coming down with something and the next day I had a seizure (my first one ever). I was sent to hospital and stayed there for several days. This post record some interesting observations both as a ME/CFS person and a person with an unknown virus (not COVID-19) that echo some aspects reported for COVID-19.

Onset

I happened to be wearing a watch (Cheap $18 watch from China) that records my pulse and blood pressure every hour. This is what was recorded. Impressive changes

Tests

The symptoms presented like sepsis, so I was placed on multiple high dosage antibiotics. Testing found nothing (Flu, bacteria, and even a spinal tap to check for meningitis). Many CRT and MRI scans. Nothing was found so the most likely cause was a viral infection of unknown type.

The fever lasted for about 3 days. I was given beta blockers, heparin etc.

Blood Sugar

It was measured by the ambulance crew and was at the high end of the normal range. For the next three days it was quite high outside of the normal range. On day 4 it returned to the middle of the normal range.

This is significant for COVID-19, because people with high blood sugar (diabetes) have a higher fatality rate. I suspect that the same increase of blood pressure pushes things still higher to the lethal range in some.

My Glucose levels — it was below 100 when the ambulance picked me up

C-Reactive Protein

If your examine my post on another blog on symptoms, you will see that high values of c reactive protein are associated with higher death rates for Covid-19 [PubMed]

C Reative Protein levels

Blood Pressure and Pulse

These stayed high and were still abnormally high at discharge. I started on supplements proven in studies to lower blood pressure, and they helped quickly but BP stayed erratic (jumping from normal to high for 2 hrs and then back), just less so over time.

A reader referred me to this study of MERS-CoV, another Coronavirus. The item that helped was resveratrol, which also lowers blood pressure (may be the mechanism it works thru).

Discharge

The moment that I got home, I did a microbiome test (Thryve) with a primary focus on correcting changes from the antibiotics. For the abnormal high blood pressure, I hit it with literally everything that was documented (see here for the list). Blood pressure and pulse initially went back to normal and then started jumping around with no apparent explanation at the time.

Oops on Supplements

I received my Thryve microbiome results and was not surprise to see the chart shown below. It indicated that the jump of blood pressure was a result of microbiome changes induced by the virus.

BP jumped due to virus induced changes of the microbiome

I then identified which shifts were key:

The interesting thing was that comparing the recommendations for this mixture and the studies, we had good overlap — but a few appear on the avoid list. I removed those from my supplements, and things improved more.

It illustrates that results from the general population may not apply to an individual. I had a subset of the high BP bacteria and being specific to those bacteria is preferred.

Hypercoagulation vs Pulse and Blood Pressure

One of the things that I noticed was that my 02 saturation was not the normal 99%. A rock steady 99%.

  • When my pulse and BP went to normal for a few hours, O2 dropped to 94%
  • When my pulse and BP went high, my O2 returned to 99%

Conversations with Dave Berg, Hemex Labs, came back. Infections often trigger coagulation (blood thickening). The light went on! The increase of both pulse and blood pressure may be a response to the low O2 level and an attempt to restore O2 levels.

As a side note, the hypercoagulation is suspected by some to play a role in postural orthostatic tachycardia syndrome (POTS). The thick blood results in delay of blood pressure in the body resulting in mis-signalling. The rapid increase in heartbeat seen with POTS is an attempt to compensate.

Heart rate and blood pressure work together to keep the blood flowing at a healthy pace, no matter what position the body is in. People with POTS cannot coordinate the balancing act of blood vessel squeeze and heart rate response. This means the blood pressure cannot be kept steady and stable….. Patients may develop POTS after a viral illness, 

Postural orthostatic tachycardia syndrome

I know from ME/CFS days that I have an inherited coagulation defect [Prothrombin G20210A or factor II mutation]. I am one of the lucky ones because there are known substances that will compensate for my particular defect: Piracetam, with tumeric being a secondary choice. I proceeded with 1200 mg of Piracetam with each meal. O2 levels went up, pulse and BP went down more. See below

BP and Pulse stayed in sync

I have a follow up in 2 weeks with my MD and hope to get some heparin to take sublingually (under tongue, not by needle) to further clear the hypercoagulation.

Virus and Coagulation

Bottom Line

It was interesting to see that this unknown virus caused changes in blood sugar and blood pressure. For COVID-19, there are higher death rates (about 9-10%) for people with diabetes (high glucose) and hypertension (high blood pressure) – I suspect that COVID-19 pushes these to potentially fatal levels.

Takeaways: reducing BP and blood sugar proactively and aggressively may be a good strategy. High BP may be connected with hypercoagulation (which may be sub-clinical, i.e. not severe enough for physicians to take action).

lassesen 7:12 am on February 29, 2020  

ME/CFS Corvid-19 Death Rate: 4.5%

In short, ME/CFS patients are older. Corvid-19 kills older people more often (over 20% in some age ranges). This computes the risk over all ages with ME/CFS. ME/CFS is not causing this high rate, patient ages are.

For reference, Flu Death Rate from CDC for 2018-2019: (=34,157/35,520,883) or 0.0962%. So the risk of death is 46.8x more

This is based on the following studies:

The methodology was to obtain the incidence rates for CFS/ME for items like:

Then obtain the ages and numbers in each age bracket with ME/CFS and then apply the following:

Note that even for the youngest are group, the chance of death is 2x the 2018-19 risk for flu.

As of this morning, there is a very strong statistical model saying that it will go pandemic with every country severely infected. By April 1st, there may be more cases outside of China than in China.

lassesen 8:41 am on February 22, 2020  

C. Jadin Resources

This is the protocol that was responsible for one of my remissions. My current belief is that what she termed “occult rickettsia infection” is “post-infection stable microbiome dysfunction”. Regardless, the treatment works in a high ( > 75%) of ME/CFS patients. The treatment was evolved prior to the microbiome entering research, using real patients over many years at the Pasteur Institute for Tropical Medicine.

A disease called fatigue by [Jadin, Cecile]
https://www.amazon.com/disease-called-fatigue-Cecile-Jadin-ebook/dp/B00ERB5AYY

Objective: To demonstrate the probable role of intracellular bacteria like Rickettsiae and Chlamydiae in the development of certain chronic psychopathological conditions and according to the efficiency of antibiotic regimes (minocyclines and/or macrolides). The letter aim is based on the fact that all the patients that I have seen since 1981 had a sera reaction positive for Rickettsiae and/or Chlamydiae using the micro-agglutination on blade technique of P. Giroud and M.L. Giroud (MAG) by Prof. J.B. Jadin of Antwerp, Belgium with special antigens cultured on guinea pig lungs and chicken embryos. Methods: This is an open study which began in 1981 in a private medical practice, not versus placebo; but with random choice. Treatment was for a minimum of six months (minocyclines and/or macrolides together with vasodilatory medication; chloroquine; warm baths). Group one: 98 CFS cases; women: 78, men: 20; for 67 cases, the ancientness of symptoms is more than 2 years. Group two: 59 psycho-somatic cases; 5 schizophrenia; 3 borderline; 10 children with aggressivity, excitement; 1 autistic child; 1 delirium with relapses. Results: Group one: 79.5% good and very good results; 4.1% fairly good; 16.4% failed. Group two: 82.3% good and very good results; 2.5% fairly good; 15.2% failed. Conclusion: This diagnostic and therapeutic study began in 1981. All of the Dr. Bottero’s therapeutic results are confirmed since 1991 by Dr. Cecile Jadin of Randburg (South Africa) for more than 3000 CFS and other psychopathological states (300): Sydney 98 CFS Conference, Australia. We have shown that Rickettsiae and Chlamydiae are probably causative factors in many “psychopathologies.”

Journal of Chronic Fatigue Syndrome . Available from: https://www.researchgate.net/journal/1547-0660_Journal_of_Chronic_Fatigue_Syndrome [accessed Feb 22 2020].

Notes from a Patient

Located here: http://lassesen.com/documentation/

lassesen 5:12 pm on January 29, 2020  

FastQ Processing Comparisons

David M. ask me about comparing results from different providers of FastQ to Taxon. I had coded it out and was unhappy with what I saw and did not post about it . I had missed a bug and while the link was there – it would error out. That bug is now fixed, and you may use it..,

Select the ones to compare — it should be the same FastQ file for all. In this case I am processing a uBiome FastQ file (so that is a choice)

Click Compare. What you see may explain my earlier post, The taxonomy nightmare before Christmas… This is the SAME DIGITAL DATA being processed thru 4 different software applications …

MicrobiomeSight did not provide taxons so a text match up was attempted (prone to errors)

Bottom Line

Standards seekers put the human microbiome in their sights, 2019
lassesen 5:57 am on January 29, 2020  

Child Autism microbiome over time – Part 3

In my last post, End Products and Autism, etc, I looked at the end product shifts seen in autism patients uploaded to my analysis site. In this post, I am going to look at the significant ones over time for this child.

The process is simple, go to compare samples, select the desired ones and click [EndProduct Time Line], as shown below.

http://microbiomeprescription.azurewebsites.net/email/compare

I will do all of those reported in the post above and on the page cited.

Watchout for Normal for Age!

We are dealing with a child, and should first look at the pattern seen for children. We do not have enough samples at the moment to be able to drill down into children with autism (as stated on the page).

Similarly, we cannot drill down further into autism until we get more samples.

A fishing expedition

The end products identified are the most likely involved with autism. More probable – not a certainty. Going thru the many charts below, I noted:

  • Between Feb 14 and April 26, 2019 there was major changes visible on many charts that cascaded onwards.
  • It may have been triggered by an increase in Acetate or Lactic Acid shown on the Feb 14 sample
    • DAO and GABA jumped massively on Apr 26, dropped down but slowly increasing afterwards
    • GABA
  • Formic acid, Thiamine and Urolithins kept increasing after that

April 26th Notes: Diet: up to this date still eating mainly soups and all organic home cooked meals and healthy snacks fruit and nuts. Taking full set of recommended supplements tho experiencing nose bleeds.
Feb 14 Notes: After Sample started probiotic L.reuterei and camel milk. Stools consistency soft, solid. Diet: consisted of vegetable soups and also had introduced celery juice in the mornings.
Addendum ” we stopped for a week because I started seeing more irritability as result. ” resumed.

I would suspect that Lactobacillus Reuterei

From 8 bins and 16 bins

Milestone

The data driving end-products is not as complete as I would like it (if you know of a good source of end product to taxa, please email to me!). I refer to it as experimental because of the lack of solid data. Many of the taxa reported to produce some end products are not reported on by 16s labs.

For this person, we see that Lactobacillus Reuteri appears to have triggered significant changes. “Role of Lactobacillus reuteri in Human Health and Diseases“[2018]. It would account for the increase of Lactic acid and periodic courses may be advantageous. Also with L. Reuteri, “acetate is produced at much higher concentrations 76.” 

The production of formic acid is a little concern. This does not mean you will find high levels in the body; you may find some very fat bacteria that feeds on it and it’s salts ( Formate) .

As a result, I want to identify the bacteria that is causing this. First a Visual:

Then I added a new page,

Clicking and then selecting the End Product
We see what the high producers are.. child and parent (a double count scenario)
We can see that almost every sample is sky high

Going over to Peter D’Adamo Data Punk site, we see that this bacteria inhibits a lot of things:

At this point we have several choices – we could click on Eubacteriaceae or Eubacterium and pick up items to add or remove from the menu. Instead, recall in my Child Autism microbiome over time – Part 2 post, we had a hand picked taxa. I am going to add it to that existing mixture:

Doing it on the already selected taxa
Just click the two, and click Create a custom
Our new collection of bacteria taxa that we wish to modify

We now have similar, but also different suggestions then before. The artificial intelligence engine attempts to find the optimal combination for the above bacteria

Note that we have contrary results for the species lactobacillus rhamnosus (probiotics) versus a specific strain lactobacillus rhamnosus gg (probiotics)

Explicit manipulation of end produces is beyond my comfort level. Formate is water soluble, so this may be a moot issue apart from changing pH. I will leave that speculation to medical professionals.

Bottom Line

This is my first detailed end product analysis connected to a symptom or medical. I ended up writing two more analysis page with the final results being interested. This autism child has one bacteria extremely high and because of using end products we discovered that it would end up with a high amount of formic acid altering the gut and from the literature, also see that it would alter the gut pH — causing more changes of gut bacteria. I have seen another “out of control bacteria (top 2% of values)” in another child with autism (but totally different bacteria) after a different probiotic was started. This may be just two unusual cases, but I thought that it should be mentioned.

We ended up combining several parts of this analysis into one hand picked taxa to adjust and have a good list of changes to consider in consultation with your medical professional.

P.S. One more sample result arrived and was uploaded. The predicted symptoms are matches to earlier ones. I will leave it to the mother to inspect the updated charts shown above.

The microbiome of autistic children is challenging because of several factors:

  • Medical studies (over a dozen) do not replicate each other (see Technical Study on Autism Microbiome)
  • Not many samples to work with using citizen science
  • There is a feeling of “instability”

On the positive side, by this series of post – we can make logical deductions of experiments that may be worthwhile. With regular 16s testing (always the same lab please!!!) you can actually see if something made a difference (for better or worst).

A big KUDO to the mother for keeping detailed daily detail notes and granting permission to use the child’s microbiome results.

Feed Back

I feel I got to keep thanking you for all your observations regarding the data. These give me huge clues in which I can find more bread crumbs in how to better help my daughter.

In you 3rd part of your observations on end products you mentioned that Formic acid was increasing, so from studies that is linked to inflammation in the large colon and increase in bad bacteria.  But I also found an interesting study that indicates the following:

“ This study was conducted to explore the in vitrofermentation characteristics for different ratios of soluble to insolubledietary fiber in pig fecal microbiota. The fermentation substrates consistedof inulin and a non-starch polysaccharide mixture and were divided intofive groups according to different soluble dietary fiber (SDF) to insolubledietary fiber (IDF) ratios (SDF 25, 50, 75, and 100%). With the increasedSDF ratio, the total gas production increased, and the pH in the substratedecreased as the fermentation proceeded. The concentrations of lactic acid,formic acid, and acetic acid increased in the high SDF ratio group, whereasthe concentrations of propionic acid and butyric acid increased in the lowSDF ratio group. The genera Clostridium_sensu_stricto_1, Ruminococca-ceae_NK4A214_group, Christensenellaceae_R-7_group, and Rikenella-ceae_RC9_gut_group were enriched in the high SDF ratio group.Correlation analysis indicated that these differential bacteria had thepotential to degrade polysaccharides. These results revealed that high SDF ratios could stimulate the proliferation of fibrolytic bacteria, which in turn degrade fibers to produce organic acids and monosaccharides. Collectively, these findings add to our   understanding of the mechanisms responsible for interaction the rational use of dietary fiber.”

This is also giving me a clue on the type of food that may be contributing to the increase of Formic acid..  as I explore the type of diet I had changed to e.g. no wheat  I reduced the intake of insoluble fiber, then I furthered explored what level of IDF vs SDF foods I have been giving my daughter.  I’ll be looking at my food logs to see the trend.  

THANK YOU!  As I continue in my search.