Month: November 2024

CFS with Brain Fog

Backstory:

Hello, I’m a 21-year-old with a moderate case of CFS. Currently, I’m having serious problems with concentration, reading, memory, and executive function to the extent of needing a caregiver. I react to any food with neurological symptoms and gas, and my energy production is so impaired that I get hungry just two hours after a large meal. I would like to hear your analysis of the sample, especially your opinion about the sky-high amounts of Bilophila wadsworthia.

At 13 years old, I started having hemiplegic migraines with aura, including paralysis, speech, vision, and orientation loss due to an ATP1A2 mutation. These were thought to be incurable until I randomly found an off-label local medicine, metamizole, which is prohibited in the US, Canada, and the EU but is available in my home country, Ukraine. This medication was effective in mitigating the aura. I started taking it every day for four years starting at age 16. Recently, I learned that it increases prostaglandins and has an immunosuppressant effect like NSAIDs in general. I suspect that my daily use of this medication may have contributed to developing CFS and hypersomnia through unchecked mucosal infections.

I was also diagnosed with 160,000 copies of HHV6 in my blood via PCR, which persisted for years (I stopped testing for it). I tried valganciclovir, artesunate and IFN-a, which did nothing but further worsened my baseline. A year and a half ago, I started Joshua Leisk’s Born Free protocol (https://bornfree.life/download/BF_Protocol.pdf), which improved my metabolic situation significantly. However, I coincidentally started living in an unhygienic, mold-infested environment, and subsequently had GI and Eustachian tube infections. After taking nifuroxazide, amoxicillin, and metronidazole a year ago, my condition worsened to a moderate level, and I haven’t recovered since.

I suspect that gut issues are the cornerstone of my problems, but I am quite lost lost regarding how to handle them. I am eager for any new information.

The model that I use for ME/CFS is some event (stress, food poisoning, virus, inoculation or dozen of other possible events) cause the microbiome to shift in response. The shifts can result in a feedback loop that keeps this “evil microbiome” shift going. A percentage recover naturally over time, and we have a longitudal study from Bergen Norway to illustrate this. The trigger was giardiasis for a large number of people. A medicine like metamizole on a continuous basis can easy cause this to happen.

Analysis

We have two samples available, so let us look at the before and after antibiotics comparison. My impression is that the antibiotic made things worse. The latest sample has more items out of range despite having ~20% less bacteria reported

Since we are nominally dealing with ME/CFS, we can use the cross validated suggestions to get conservative suggestions of what may help

The result is a massive list!

We will backtrack to “Just Give Me Suggestion Including Symptoms” so we can rank order these suggestions.

The top items are antibiotics, with 60% being those used to treat ME/CFS (i.e. on the above cross validated list). I tend to follow Jadin’s approach so, do one of those marked [CFS] for a course (7-10 days) and the next month(3 weeks off), move to a different one. After the 3rd one, get a new microbiome test to see the next course adjustment.

Probiotics are dominated with Bifidobacterium species. I would tend to do 3 weeks on one strain between antibiotics, working up to a dosage of 50 BFU. At present, my favorite source is Maple Life Science™: they ship worldwide, typically the packages arrive with manufacture dates 4-6 weeks before (thus LIVING probiotics), and very reasonable cost. Yakult and Kefibios can be difficult to obtain in some countries.

Going over to KEGG suggested probiotics and although we are approaching it from a totally different path, we have consensus.

For prebiotics, just three stand out, take them with the above probiotics

For vitamins (can be taken continuously), I would suggest adding them one at a time (every 3-4 days) in case some create significant (good or bad) reactions.

For flavonoids, the list is very ME/CFS typical.

Second Pass – Cross Validated Suggestions

I picked these from the short list of options in the old UI.

The number of bacteria matches were relatively few.

The suggestions are shown below. Note that Lacticaseibacillus casei and Lacticaseibacillus paracasei shirota. Are on this list, just as they were above. Avoid other lactobacillus probiotics.

Questions and Answers

Some questions:
— what are your thoughts on the sky-high levels of Bilophila (any specific advice on managing that?) and the very low overall species diversity. I did some troubleshooting with a CGM, and every time I eat some animal fat—and to a lesser extent, animal protein—after carbs, I experience a hyperglycemic spike. I attribute that and my brainfog to a Bilophila overgrowth (H2S & acetaldehyde). When I’m on a vegan diet, my blood sugar is generally perfect, except for one hypoglycemic event at night but it’s really problematic to sustain this diet long-term.
— also, which advice here is aimed at increasing lactobacillus abundance as the recommended probiotics are mostly bifido?

Response

Here we hit a philosophy crossroad.

  • The road most travelled is focusing on the bacteria most heard about and trying to address them one by one.
  • The road that I take is to ignore this chatter, and aim to adjust everything in one pass using mathematical models.
    • Often I have read that something like Lactobacillus increases for a subset of people if other bacteria are present, (or absence).
    • I view this approach is most likely to cause desired changes and not chasing this bacteria or that bacteria.
Microbial Interdependence

Microbial interdependence occurs when different bacterial species rely on each other for growth or survival. This can happen through various mechanisms:

  • Metabolic cross-feeding: One species produces metabolites that another species uses for growth.
  • Signaling interactions: Chemical signals from one species trigger responses in another.
  • Modification of the environment: One species alters the local environment in ways that benefit another species.

Given that concentration is an issue, there is a high probability that high d-lactic acid is involved. This would cause me to suggest avoiding lactobacillus probiotics entirely. It is impossible to determine which retail brands produce d-lactic acid.

Bottom Line

Go slow, slowly increase dosages, keep track of your reactions on paper (or electronically). Some suggestions will have no effect, others may have dramatic effects.

Postscript and Reminder

As a statistician with relevant degrees and professional memberships, I present data and statistical models for evaluation by medical professionals. I am not a licensed medical practitioner and must adhere to strict laws regarding the appearance of practicing medicine. My work focuses on academic models and scientific language, particularly statistics. I cannot provide direct medical advice or tell individuals what to take or avoid.My analyses aim to inform about items that statistically show better odds of improving the microbiome. All suggestions should be reviewed by a qualified medical professional before implementation. The information provided describes my logic and thinking and is not intended as personal medical advice. Always consult with your knowledgeable healthcare provider.

Implementation Strategies

  1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
  2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
  3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
  4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why

Professional Medical Review Recommended

Individual health conditions may make some suggestions inappropriate. Mind Mood Microbes outlines some of what her consultation service considers:
A comprehensive medical assessment should consider:

  • Terrain-related data
  • Signs of low stomach acid, pancreatic function, bile production, etc.
  • Detailed health history
  • Specific symptom characteristics (e.g., type and location of bloating)
  • Potential underlying conditions (e.g., H-pylori, carbohydrate digestion issues)
  • Individual susceptibility to specific probiotics
  • Nature of symptoms (e.g., headache type – pressure, cluster, or migraine)
  • Possible histamine issues
  • Colon acidity levels
  • SCFA production and acidification needs

A knowledgeable medical professional can help tailor recommendations to your specific health needs and conditions.


6x COVID Indections + Rosacea

Back Story

My journey to how I ended up where I am now is that I’ve always been one to catch illnesses like colds, flus, and stomach bugs easily. I was also frequently medicated with antibiotics for many years as a kid. Looking back, of course my microbiome is a mess. 

To date, I have had COVID 6 times (that I know of/positive tests – there was probably more that didn’t “show up” or that I may have dismissed as a cold). 

The first time I had Covid was January 2020, before it was “a thing”. It was later confirmed that it was indeed COVID, with an antibody test sometime in February-March 2020 when I donated blood. I was the sickest I’ve ever been in my life (26yo then, I’m 30 now). My main symptoms were feeling out of breath and lightheaded, as well as gastrointestinal (diarrhea and vomiting) – which at the time, no one was acknowledging that COVID could have any gastro symptoms, so I kept getting dismissed that it couldn’t have possibly been COVID. I was sick for a solid week and a half and it took me about 8 weeks to get back to feeling somewhat normal and not out of breath etc. 

 I’ve missed so much work because of this illness and I just keep catching it – the most recent time being just a month ago. 

I developed the skin condition Rosacea around late 2022-early 2023 which I believe is microbiome related – I’ve tried many topical prescriptions that don’t do a dang thing, and it has since spread to my eyes and I now have Ocular Rosacea as well.

 I’ve always had chronic constipation but it is worse since 2020. I have fatigue and am always tired, no matter how much I sleep. At one point I had high iron, so I was told to donate blood to lower it, but then my iron and ferritin fell so low that I was told to stop and instead take iron supplements to get my iron and ferritin back up – which I cannot tolerate, because it causes stomach issues for me. 

I’d love to figure out how to really improve my microbiome and finally heal from all of this. I’m constantly living in fear that I’ll catch COVID again and lose any progress I’ve made. 

Analysis

  • Rosacea is a chronic inflammatory skin condition that can have systemic effects and comorbidities. While not directly linked to ME/CFS or long COVID, it shares some characteristics of chronic inflammatory conditions. I have encountered several ME/CFS with it
  • Constipation is commonly associated with ME/CFS (Myalgic Encephalomyelitis/Chronic Fatigue Syndrome).

Both are suspected to be cause by imbalance of gut flora (microbiome).

We see a lot of pattern matching to other people with the same symptoms.

But since we are dealing with a situation with some cross-validation data being available (i.e. lists of things with studies that helps with the symptom/diagnosis), I like to start there. On [Changing microbiome tab].

Updated Analysis

The original draft was done before the Simple UI was released. There was 6 forecast matches over 70%, so I went with symptoms, Despite having 11 symptoms, only 9 bacteria was selected.

The suggestions are shown below

Probiotics

These are the top items, some can be hard to get. Some of my usual sources are:

The above are based on how they are known to alter other bacteria from published studies. Next I swing over to KEGG to see which probiotics can provide metabolites and enzymes that the person is low in. This is a complimentary approach that does not depend on a study being done, rather working from the DNA of the microbiome. I have annotated the above with their [Metabolite/Enzymes] scores above. The highest lactobacillus was 4, Bifidobacterium [7]. One bacillus ranked high, but is not easily available as a probiotic: Bacillus thuringiensis -[15/9]. My preferred sequence would be to start with B.Subtilis and then B. Coagulans.

Foods

The food menu suggests that Turkey and Chicken are the best meats. Kiwis and Soy are next. To avoid: carrots, beans, sweet potatoes,

Vitamins are the usual for ME/CFS

One word of warning — do not use B-Complex. They contain some B-vitamins that are to be avoided. Get the specific B-vitamins shown.

Postscript and Reminder

As a statistician with relevant degrees and professional memberships, I present data and statistical models for evaluation by medical professionals. I am not a licensed medical practitioner and must adhere to strict laws regarding the appearance of practicing medicine. My work focuses on academic models and scientific language, particularly statistics. I cannot provide direct medical advice or tell individuals what to take or avoid.My analyses aim to inform about items that statistically show better odds of improving the microbiome. All suggestions should be reviewed by a qualified medical professional before implementation. The information provided describes my logic and thinking and is not intended as personal medical advice. Always consult with your knowledgeable healthcare provider.

Implementation Strategies

  1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
  2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
  3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
  4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why

Professional Medical Review Recommended

Individual health conditions may make some suggestions inappropriate. Mind Mood Microbes outlines some of what her consultation service considers:
A comprehensive medical assessment should consider:

  • Terrain-related data
  • Signs of low stomach acid, pancreatic function, bile production, etc.
  • Detailed health history
  • Specific symptom characteristics (e.g., type and location of bloating)
  • Potential underlying conditions (e.g., H-pylori, carbohydrate digestion issues)
  • Individual susceptibility to specific probiotics
  • Nature of symptoms (e.g., headache type – pressure, cluster, or migraine)
  • Possible histamine issues
  • Colon acidity levels
  • SCFA production and acidification needs

A knowledgeable medical professional can help tailor recommendations to your specific health needs and conditions.

Virus caused ME/CFS

ME/CFS has many causes, a very common cause are virus (in the case of Long COVID, the COVID virus).

Back Story

A quick summary of my story: I got ME/CFS after two viruses about a month apart in late 2016, when I was 27 – one upper gastrointestinal and one upper respiratory. After struggling to work for a couple of months after my body eventually gave up and I had to be signed off sick, and then eventually let go. I haven’t returned to any work since. I would say I am at the moderate end of the spectrum – able to socialise outside of the house on occasion as long as transport isn’t too strenuous, but not well enough to do things on a consistent basis, with obviously lots of rest all the time. Since then I’ve been on a journey seeing various doctors mostly to no avail, although not for a few years now. 

My main symptoms now: 

  • Fatigue
  • Muscle weakness 
  • POTS
  • Unrefreshing sleep 
  • Various mild / moderate pain
  • Very prone to overheating / sweating

I take 40mg Duloxetine once a day, ostensibly for nerve pain although it has helped significantly with my overall energy levels and wellbeing, moving me from severe to moderate from when I started taking it a few years ago. 

It’s worth pointing out that over the course of my illness I have tried several probiotics and things suggested with the gut. These are as follows (if I remember correctly): 

  • Optibac
  • BioKult 
  • Generic acidophilus probiotic 
  • GI Synergy antimicrobials
  • Yakult (more on that in a minute) 

Every single one of these has caused these symptoms of varying severity: 

  • Increased blood pooling 
  • Sore throat 
  • Flushing
  • Fatigue
  • Disorientation 
  • General malaise 

So in general I have stayed away from things to do with the gut because of these bad experiences. Yakult is actually something I stopped only recently – I read your blog post about d-lactate and given it’s so cheap and easy to get hold of decided to give it a go. I would say that while the other probiotics caused those symptoms almost on the first or second dose, with Yakult it took a lot longer to set in. I took it for 3 weeks before I finally realised that I was at the same place symptom-wise as the others, it just took me much longer to get there. A shame as it i was a low-cost and easy thing to try. They’re obviously all doing something! Just not what I’d like, haha. 

Review of Back Story vs Microbiome Sample

Filtering by reported symptoms yield just two bacteria, both low: Lactobacillales and Natronincola. Suggestions were Barley, Oats, whole grain diet, {Reishi Mushroom},Slow digestible carbohydrates. {Low Glycemic}.

I did the simple suggestions option since the number of symptom matches to symptoms prediction was low. We found 43 bacteria out of range. None of the following probiotics were on the recommended list: Optibac, BioKult, Generic acidophilus probiotic, GI Synergy antimicrobials, Yakult

Going over to KEGG Computed Probiotics Report, we have these being the top one

Working down the list we have:

  • Lacticaseibacillus rhamnosus
  • Lactiplantibacillus plantarum
  • Limosilactobacillus reuteri – On main suggestion list

Since economics is cited, I would suggest ordering one bottle of each from Maple Life Science. They are direct from factory to retail customers; ships world wide; no shipping costs. Cost per bottle is around $9

  • Limosilactobacillus reuteri
  • Lactiplantibacillus plantarum
  • Lacticaseibacillus rhamnosus
  • Bacillus Subtilis

For the other ones, see how you react to these first. My usual suggestion is one capsule for ONE of these on the first day, increase according to your reaction. If adverse reaction, move on to the next one. Once the bottle is empty, go to the next one.

Personally, my own ME/CFS experience favors Mutaflor — but it created a massive herx for 2 weeks; so I tend to suggest moving it to the very end.

Other issues

I have no information on Duloxetine impact on the microbiome. Other suggestions have many familiar in treating ME/CFS over the last 30 years. The include:

Unusually, B-vitamins are not high on the list. If you take them, keep to Vitamin B1,B2 and B12.

Going over to the Food Site we have these nutrients at the top

The first one, Resveratrol, is found in fresh grapes in the supplement form is not desired. The second one is mainly in raw Chicory . The third one is found in Black elderberry (and a small amount in Pomegranate). The fourth item, (-)-Epigallocatechin, is found in Green/Oolong Tea and Broad Beans. The next one, Cyanidin 3-O-xyloside, is mainly in Black chokeberry (and a small amount in Blackberries). Hesperetin is found in Lime and Oranges (not orange juice). Resistant starch is in Broad Beans, Lentils and Peas. Syringaresinol is found in Rye (i.e. whole 100% rye bread) and the Swedish Cloudberry (likely out of season now). Diosmin is found in Hyssop (I tend to buy it as a supplement).

As a FYI, my regular “ME/CFS preventative” diet is usually heavy in grapes or Resveratrol (depending on season and price); 100% Rye Bread; Broad Beans and Lentils; Hesperetin and Diosmin.

Questions And Answers

  • Q: The herx / die off stuff do you have any guidance on that? What I meant was: given my adverse reactions to any probiotic I have tried – whether that’s on the same day after initially taking, or eventually building up after several doses – how can I tell the difference between a reaction that’s bad and should cease taking it, or supposed “die off” symptoms, if you see what I’m saying. Basically how to tell the difference between stopping needing to stop taking a probiotic due to the symptoms its producing, or pushing on, and seeing if it tails off. Does that make sense? 
    • Your question makes a lot of sense. I have done a few posts on that:
    • A short version for probiotics is this:
      • If the adverse effect is ongoing 18 hours later, it is likely an adverse reaction or feeding bad bacteria. Many studies find that some probiotics are not detectable after 24 hours (not true for all of them).
      • The duration of the reaction should be decreasing each day. You should feel a little better after the effect ebbed each day. Often, there can be a quick ending of the reaction. If it increased or do not change, it is likely an adverse reaction or feeding bad bacteria.
  • I have improved the Lookup Modifier Page to flag what a probiotic is impacting. You need to break a mixture apart and examine it parts. Most of his probiotics were mixtures containing L. Acidophilus. Note that Sutterella is in common with both

Postscript – and Reminder

I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”.  I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.

I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.

The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.

Suspect Lyme Disease post antibiotics

Backstory

As I’ve been suspected to have Lyme disease, I have taken antibiotics for several months which have damaged my microbiome. Now I am taking antibacterial herbs.
* As my brain fog severely increased, I need your help to adjust my strategy. In addition, there are some specific questions:
I am contacting you as I have done a new microbiome analysis with BiomeSight. I haven’t been doing well in addition to my previous health issues. As I’ve been suspected to have Lyme disease, I have taken antibiotics for several months which have damaged my microbiome. Now I am taking antibacterial herbs.
As my brain fog severely increased, I need your help to adjust my strategy. In addition, there are some specific questions:
❔mutaflor isn’t among the suggestions done. Would it be a good thing to add it ?
❔how long should I wait between probiotics and antibacterial herbs ?

From Email

Analysis Of Data

I have a pretty fixed attitude to Lyme

  • It’s Lyme only with a very clear laboratory result (i.e. tests for actual Borrelia species and strains and conforms to the rest of CDC criteria).
  • “Chronic Lyme” is likely post-infection syndrome and the use of “Lyme antibiotics” can often do more harm than good. “Suspected Lyme” is a red flag that the medical practitioner is outside of their depth.

We have three samples available. There was some apparent improvements from earlier samples (

Comparing current sample to the first sample is shown below. The number of bacteria reported is almost half of the prior test, making comparison difficult, but my impression is that there was some improvement.

Looking at the new symptom matching comparison , we see some significant drops.

Going Forward

Since symptoms have been entered, we will go with [Beginner-Symptoms: Select bacteria connected with symptoms]. This results in 29 bacteria being identified (about 8% of the bacteria – my preferred range is 4- 12% being flagged to be of concern).

The top suggestions are below which are heavy in fiber and beta-glucan. A common pattern with post-infection syndrome.

The avoids echo this high fiber approach

Probiotics

We actually have three lists to compare:

The numbers in the [ ] are the number of compound that are low that the probiotic produces. Enzymes shortage usually leads me towards probiotics because they are producers of many enzymes. Most of these enzymes are not available as supplements. When there are shortages, bacteria misbehaves… “when the manager is empty, horses bite”

My suggestion for rotations (1 probiotic for 1-2 weeks and then move on to the next)

Alternative Paths

At this point, we branch into two additional paths — one by using Kyoto Encyclopedia of Genes and Genomes (KEGG) data on compound being produce and consumed by your microbiome. With KEGG we look for probiotics that can provide enzymes etc that you are deficient in. Why these alternative paths? Simple, there is not enough data available so we use inference.

The second path is going to the food site to identify foods rich in suggested nutrients. The foods may not have been used in studies, but the dominant nutrients in the foods may have been studied.

KEGG

The top suggestions are below. #1 item is common for ME/CFS, Mutaflor is available in some countries in Europe, I warn people that it may cause a major die-off / herx reaction. Symbioflor 2 is the same probiotic species but at ~ 1/100 of the BCFU and unlikely to cause die off. These are reasonable “2nd rank” probiotics to try. The evidence is by inference and not direct study.

Food

Going to the food site, we find walnuts, almonds,cocao/dark chocolate, and beef at the top of the list. The following food groups should be added to the menu also:

Questions

❔ Brain fog

  • Usually this is due to d-lactic acid which is produced by some Lactobacillus species but not by Bifidobacterium and others. You may wish to skip those in the above list. Thick blood is another common cause for brain fog.
    Other things to try (assuming d-lactic is the cause):
    • Sodium Bicarbonate (baking soda)
    • Thiamine (Vitamin B1) – Low on Avoid list
    • Calcium Supplements – Low on suggestions list

❔mutaflor isn’t among the suggestions done. Would it be a good thing to add it ?

  • Mutaflor is at present on the avoid list but top of the KEGG list. It is worth doing a short trial to resolve if it is good or bad for you. I put it at the bottom of the list, in the hope that the other probiotics would cause changes that it can use.

❔how long should I wait between probiotics and antibacterial herbs ?

  • Typically I suggest 2-3 weeks of probiotics and then a switch. Above we have a variety of nuts (remember peanuts are not nuts) and other foods that are not deemed antibacterial. My general impression of the suggestions is that encouraging good bacteria (instead of killing bad bacteria) is the desired direction.

Postscript and Reminder

As a statistician with relevant degrees and professional memberships, I present data and statistical models for evaluation by medical professionals. I am not a licensed medical practitioner and must adhere to strict laws regarding the appearance of practicing medicine. My work focuses on academic models and scientific language, particularly statistics. I cannot provide direct medical advice or tell individuals what to take or avoid.My analyses aim to inform about items that statistically show better odds of improving the microbiome. All suggestions should be reviewed by a qualified medical professional before implementation. The information provided describes my logic and thinking and is not intended as personal medical advice. Always consult with your knowledgeable healthcare provider.

Implementation Strategies

  1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
  2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
  3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
  4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why

Professional Medical Review Recommended

Individual health conditions may make some suggestions inappropriate. Mind Mood Microbes. outlines some of what her consultation service considers:
A comprehensive medical assessment should consider:

  • Terrain-related data
  • Signs of low stomach acid, pancreatic function, bile production, etc.
  • Detailed health history
  • Specific symptom characteristics (e.g., type and location of bloating)
  • Potential underlying conditions (e.g., H-pylori, carbohydrate digestion issues)
  • Individual susceptibility to specific probiotics
  • Nature of symptoms (e.g., headache type – pressure, cluster, or migraine)
  • Possible histamine issues
  • Colon acidity levels
  • SCFA production and acidification needs

A knowledgeable medical professional can help tailor recommendations to your specific health needs and conditions.