CFS Remission | Striving for true remission of CFS, chronic Lyme, FM, IBS etc

Time 2020-12-07 06:02:11

Web Name: CFS Remission | Striving for true remission of CFS, chronic Lyme, FM, IBS etc

WebSite: http://cfsremission.com

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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 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.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.BiomeSight.com (EU based but serves the world) discount code MICRO has integrated with my analysis site with automatic data transfer. For most people it is likely the best deal.Thryve (US Based) is what I have used. Their reports may be processed here for independent suggestions. I would also recommend Joining The Gut Club group on FacebookJoining (free) The Gut Club They have a discount code for Thryve save yourself some extra dollars.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.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.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 postWe 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/ 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).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.Over this weekend I deprecated my earlier comparison tool and replaced it with more comparisons. To use this tool you need at least three samples uploaded. The comparisons available ate:You want to see what has changed from your prior samples. Typically, to see improvement or deterioration.You have an individual with challenges and have other samples from your microbiome bubble.People with shared DNA are part of your bubblePeople eating the same diet (i.e. family meals) are part of your bubbleConceptually, people with the share medical conditions could by part of the bubble. My observations is that these people should have the same symptoms not just the same diagnosis.There are four methods of comparison of one specific sample against a collection of reference samples.Values outside of the values of the reference sampleValues outside of the values of the reference sample increased by one standard deviation up and downValues outside of the values of the reference sample increased by two standard deviations up and downValues outside of the values of the reference sample that are also in the extreme compared to other samples uploaded (top or bottom 3-6%)I picked several prior samples and my latest sample for comparison. Note that Reference Samples Reporting if less than all (in this case 8), it means that there were some zero values (and thus, you may wish to ignore shifts being low for those).I tried different method and was surprise to see a long list of bacteria that have readings very different than than prior samples and also extreme values.When I want to see just what shifted without restricting to high/low values also, we get a much bigger list.This is an analysis of a parent with two children with a mixture of challenges. A person s microbiome and their DNA appears to be related. Ignoring studies, it makes logical sense. The DNA favors certain metabolites, which favors certain bacteria and the reverse. Perturbations in the gut microbiota have been linked to atopic diseases. However, the development of atopic diseases depends not only on environmental factors (like microbial stimulation) but also on genetic factors.Host-microbial interactions in childhood atopy: toll-like receptor 4 (TLR4), CD14, and fecal Escherichia coli [2010]P Parent: No ASD, nor CFS. No current IBS (I had IBS symptoms 2003-2012). Sample: BiomeSightA : ASD/CFS Sample: Thryve, FASTQ processed thru BiomeSightB : No IBS. He had SIBO in 2017. Has been in remission from PANS for about 1 year prior to sample. Sample: BiomeSightI looked first for bacteria that were high (top 6%) or low (bottom 6%) across multiple samples and found some interesting patterns:Items like Limnobacter and Amoebophilus really jumps out. They are rare, so the odds of 2 people at random having them and both being in the top 6% is about 0.002%. Adjusting for BiomeSight samples only, the odds decrease but still less than 1%.The unfortunate aspect is that of these 4 bacteria, we only have significant data on how to reduce Faecalibacterium. Checking PubMed on Limbobacterm, we see barely 40 studies with the count being low in Parkinson s disease [2018]Applying the same criteria for End Products being produced, we have d-lactate being #1. This is common with CFS and I have written about it before (see posts below). It is also likely common with ASD.For which bacteria produces which end products, see this page. I have on my backlog of features a page that makes suggestions based on end products to be shifted only. At the moment, it s a manual process of hand picking bacteria.Here, we will use top and bottom 3% since we have a lot more categories to examine. We found no shared items.The intent of this post was to look at commonality over a genetic related group of people living in the same house and likely eating the same diet.For individual suggestions by person, I would advocate doing a hand picked taxonomy and working from there. For the child with ASD/CFS, I went and did that with their sampleAs always, these are suggestions that should be reviewed with your medical professional before doing. They are items believed to have better odds of making favorable changes than picking random items to try.This is the third post dealing with my latest microbiome results. The prior two were:Microbiome Outliers looking at the new KEGG Enzyme and Modules predictions with the older End Product AnalysisMicrobiome – Other Health Measures looking at the older and traditional health analysisReducing bacteria associated with high blood pressureReducing bacteria associated with BMI/obesity Increasing Bifidobacterium which largely disappeared with the last CFS/ME flare.Target suggestions means hand picking the bacteria and then getting the suggestions based on that specific subset.This is easy to do, just go to the page and check (under include) the items and then click [Create a custom suggestion profile ] buttonI now do the same for high blood pressure. I am not surprised to see only one item because I have been using supplements shown to reduce blood pressure for a few months (seeHypertension – What we know)Last item was Bifidobacterium I do not need to do anything because it is included in the lists above.With Quick suggestions, the items below were pre-selected. You can modify them as you wishThe suggestions are generally similar but a few new items appear and the weight of some items have moved up or down.I will be working off the handpicked taxa suggestions because they are more likely to be effective for my three goals.The more focused (the fewer the goals, the better the suggestions should be because there is less noise).I admit it, I do not like many of the simplifications that I see for determining gut health. Those approaches were often the best available a decade ago; taught at universities, etc but the world of the microbiome has moved at warp speed since. This is the 2nd part of my latest microbiome results, done with reference to a ME/CFS flare in 2019. The first part was Microbiome Outliers which showcased new analysis tools.For many people with ME/CFS, simplifications will often be the limit of their cognitive ability due to brain fog. So . I support the popular simplifications on my site so there is at least some data that they can grasp.The conclusion is that GABA supplementation may have a little effect, but a major difference is not expected.For reference, my levels with active ME/CFS is below. GABA and Lactate were much lower then (and other things off).It s interesting that both counts increased. In one sense, we can see that the count of typical bacteria being used increased from 5 -> 11 -> 15. In keeping with my observation of the explosion of unusual species and reduction of common species with ME/CFS flare, this makes sense (See ME/CFS Relapse Report #8)This is an experimental measure intended to reflect general medical conditions and not ME/CFS specifically. I have no other medical conditions and the results were stable across all periods.This is nothing more than a listing of bacteria associated with one or more health conditions. IMHO, values less than 2000 are not sufficiently significant to be concerned aboutThe dominant one during the ME/CFS flare was Subdoligranulum which dropped down with recovery, 47258 > 504 > 1153. Parabacteroides are an ongoing concern but they are not ME/CFS associated but associated with weight and blood pressure two items that I am working on addressing.This is extending JasonH ranges by incorporating additional ranges from different sources. All of these ranges do not take into account diet, ethnic DNA etc. so they should never be taken as gospel rather vague waving of hands.In some cases, a value may be deemed too high by some and too low by others there is no definitive/right answer.Proteobacteria was a major concern for being too high during ME/CFS, then dropped too low and finally dropped off the list (when it was in the range that everyone suggests). The other dominant item of concern is Bifidobacterium which has been consistently close to zero ( 1%). This needs some research, because age is a factor [The faecal flora of man. II. The composition of bifidobacterium flora of different age groups] Among the vast gut bacterial community, Bifidobacterium is a genus which dominates the intestine of healthy breast-fed infants whereas in adulthood the levels are lower but relatively stable. The presence of different species of bifidobacteria changes with age, from childhood to old age. Bifidobacterium longum, B. breve, and B. bifidum are generally dominant in infants, whereas B. catenulatum, B. adolescentis and, as well as B. longum are more prevalent in adults In adulthood, the levels of bifidobacteria are lower (2–14% relative abundance) but remain stable (Odamaki et al., 2016). Gut Bifidobacteria Populations in Human Health and Aging [2016]On during further research, I see that it dropped from the expected range (4.3%, 7%) with the ME/CFS flare and have not returned yet.I have just gotten back results from Thryve. I have processed them thru BiomeSight.com giving me two interpretations of my sample. To better understand why I prefer this, read The taxonomy nightmare before Christmas…. In this post, I will look at the Thryve interpretation.Before starting an analysis, it is good to note what has happened between samples and any specific issues you are hoping to address. My last sample was in February 2020. At that point, I was likely close to full recovery from ME/CFS but still be careful. Subsequently to that sample:Two hospitalization for sepsis with lots of antibioticsLast sepsis residue included high blood pressure (hypertension).Instead of using prescriptions to address high blood pressure (I am taking no prescription drugs of any type making me an exception for someone in the late 60 s), I have been taking appropriate supplements for it (see Hypertension – What we know, where the items and studies are detailed) . Almost all of the items are anti-inflammatories also.Some weight loss (15 kilos, 30 lbs) possibly a side-effect of the antibiotics.I have noticed that I am sleeping longer and deeper. Smart watch reports sleep quality as Excellent Should I drop some of the supplements for hypertension? BP is often 100/70 today, so there is wiggle room.Any new supplements that I should consider?My impression is that I am in good health for my age. Still have weight to take off.I have added two massive sets of data from KEGG: Kyoto Encyclopedia of Genes and Genomes since February. For this post, I have had to add a few more pages to do this analysis. There are almost 4000 facets of your microbiome that are available. This is mentally overwhelming to most people. The outliers attempts to filter these down to a manageable number.Bacteria, like people, allow substitutions for work function. We need to be careful not to get caught up in specific bacteria all of your beer brew masters must be born within 10 miles of Munich . This Maori from New Zealand may be the equivalent or better job.I will start with pages that I call Outliers that is, values that may warrant deeper examination.Values that shows up depends very much on what is reported by the software looking at the sample. There are two sets of results that I want to look at:Those reported by almost everybody (i.e. 1300 samples or more). That is 97% shown aboveFor these I am concerned about very high and very low values (bottom and top 3%)Those reported by few people (3% of 1300, or 40 samples or less). If the values are high or low is not significant because their presence is the oddity.All of the outlier pages allow you is increase or decrease the ranges to be examined.My goal is to identify these items for later follow up (Medical Professional or PubMed research)Compare to February, I expected things to improve. I was actually surprise at the degree of normalization seen across thousands of measures (literally!) as shown below. February results are shown first, followed by October.If I hop back to a time that Chronic Fatigue Syndrome was active, we see a massive number of Kegg Module and Enzymes that were low (botton 3%ile)These new pages appear to work for identifying the processes that are off. Some of them can lead to immediate suggestions for supplements. For example, I noticed D-ribose enzymes on the list above, looking at more detail of this sample and filtering I see that everything connected to d-ribose is low. Logical conclusion, supplement with D-Ribose. Surprise, surprise the literature agrees! Results:D-ribose, which was well-tolerated, resulted in a significant improvement in all five visual analog scale (VAS) categories: energy; sleep; mental clarity; pain intensity; and well-being, as well as an improvement in patients global assessment. Approximately 66% of patients experienced significant improvement while on D-ribose, with an average increase in energy on the VAS of 45% and an average improvement in overall well-being of 30% (p 0.0001).The use of D-ribose in chronic fatigue syndrome and fibromyalgia: a pilot study (2006)Unfortunately, there is a lot of items that could be listed. Each one may take significant time to research.

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