Generative AI for Analysis of Gut Microbiome Tests and Personalised Treatment Advice

[SpacePenguin]

I wouldn't be too sure about that. Since we don't know what is involved in ME, anything has a potential to be beneficial or detrimental. Something beneficial in one way, such as helping a normally "good" strain might end up reducing another strain that is actually beneficial wrt your ME. No matter how safe something is theoretically supposed to be, if it makes you feel worse, pay attention to that.

Sure - I understand that. I should perhaps have written "They have only a remote chance of worsening my condition". At any rate, the stuff that ChatGPT has recommended to me are all in the very-low risk category and I haven't had any bad reactions so far apart from the obvious and almost unavoidable ones you get with prebiotics. By contrast, several doctors have got me on interventions that I realise now were low-evidence, high-risk: lexapro, modafinil/armodafinil, combo of 5 antibiotics to treat blastocystis hominis. The first 2 worsened my condition quickly but I stopped them without any lasting effects. The blasto treatment though probably did serious longterm damage.

 

[SpacePenguin]

Wow, what an experimenter. Never thought about it, but our ancestors definitely ate insects too. However, they also allegedly ate up to 200 different plants. A substrate for most varied bacteria, not available to us today.

I go out into the forest, pick clean leaves from nontoxic plants, put them in my mouth and move them around (without chewing), and even stick then up my nose. For soil exposure, I go out into wild areas, off the walking track a bit, find a patch free of obvious animal feces, scrape away the leaf litter and the first few centrimetres of soil. Then I scrape my finger tips and nails through the soil, take a small bit of that clean soil and rub it all over both sides of my hands. I rub off the excess soil, leaving a residue of soil stains on my palms and fingers. then i lightly rub my fingers and hands over my cheeks, jaw, and neck. This should all result in good exposure to beneficial microbes with acceptably low-risk of pathogenic exposure.

With none in my biome (compared to fermented food eaters, as I actually always have been), I do benefit from high count lacto- and bifido- brands. Though, I only take them after night shifts on a empty stomach before a further nap. And off I go, into grotesque continuous and at times lucid dreaming land. Without, I don't remember dreams. Though B6 and resistant potato starch were first needed, for this effect to occur now.

Supposedly, probiotics survive best when taken at the start or middle of food containing fat - helps to buffer the stomach acid. When empty, the stomach's acidity is at its highest which provides a protective barrier against microbes. Have you tried using Bifido-only probiotics as ChatGPT counselled me?

 

[pamojja]

Supposedly, probiotics survive best when taken at the start or middle of food containing fat - helps to buffer the stomach acid. When empty, the stomach's acidity is at its highest which provides a protective barrier against microbes.

I must have very low stomach acid. And have only an 8-hour eating window. Sometime eating the wrong time, I vomit. Then I realize, I actually had none. My vomit then tastes as when eaten. No acid at all.

However, usually I don't vomit after eating. Therefore, I assume, there must be much more stomach acid after meals whwn digesting just fine, than a completely empty stomach. And since no acid in my stomach on empty stomach, bacteria survive then the easiest, to reach the intestines. It's not my experience with vomiting, also by taking supplements on empty stomach, that there is any acid when empty.

As after a night-shift. My biome-result showed 0 Bifido or Lacto, though I additional eat curd, kimchi, sauerkraut daily. My ubiome showed the highest diversity, similar to under-gatherer Hadza in Tanzania, and not a western like me. Which despite highest diversity, don't harbor any Bifido or Lacto too.

Have you tried using Bifido-only probiotics as ChatGPT counselled me?

Since those Bacteria since decades don't stick anyway, I never sought out a Bifid only product.

 

[pamojja]

When one has thin mucus lining in the gut, looking at something for glycocalyx or glycosylation may be helpful.

I have seen those things mentioned over the years, but always thought the evidence was thin and the cost was high

Glycocalyx is evident. It is the outermost protective layer of artery walls. It's similar to the hair of fish, microscopic small hair, which makes touching fish's skin so slippery. The artery wall need this slipperiness too, for endless blood circulating not causing damage to the artery wall. Once damaged, cardio vascular disease begins, the disease most people die from, starts. Plaque is growing from then onward at a 30% yearly rate. And in only 10-20 years, breaks off and blocks the blood. Heart attack, stroke, or amputated leg.

https://drmalcolmkendrick.org/2018/08/21/what-cause-heart-disease-part-53-diabetes/

However, the body usually makes and repairs it with what it gets in diet. More vitamins also got from food is beneficial too. It not always has to be fancy and expensive supplements. But at least the essentials, starting with Vitamin C, or sulfur containing Chondroitin Sulfate, for example.

Glycocalyx Maintenance and Repair: Key Strategies​

Overview
The endothelial glycocalyx is a vital, protective layer lining blood vessels, essential for vascular health and homeostasis. Its maintenance and repair are crucial, especially following injury or in disease states. Several strategies—ranging from lifestyle and fluid management to pharmacological and nutraceutical interventions—have been explored to support glycocalyx integrity.

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Factors Supporting Glycocalyx Maintenance

• Normoglycemia and Euvolemia: Maintaining normal blood glucose and fluid balance is fundamental, as hyperglycemia and fluid overload can damage the glycocalyx5.
• Antioxidants: Agents such as nitric oxide, superoxide dismutase, and catalase help protect the glycocalyx from oxidative stress36.
• Albumin: Infusion of human plasma albumin supports the mechanical and chemical stability of the endothelial surface layer7.
• Glucocorticoids: These can inhibit inflammatory processes that lead to glycocalyx degradation37.
• Sevoflurane: This anesthetic has shown protective effects on the glycocalyx in some experimental models3.
• Avoidance of Inflammatory and Ischemic Insults: Preventing systemic inflammation, ischemia-reperfusion injury, and excess atrial natriuretic peptide release can reduce glycocalyx shedding457.

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Therapeutic and Nutraceutical Approaches for Repair

• Heparanase Inhibitors: Targeting heparanase-1 (an enzyme involved in glycocalyx breakdown) can help limit damage and promote repair, especially in sepsis1.
• Replacement of Glycocalyx Components: Administration of exogenous glycosaminoglycans (GAGs) such as hyaluronan and chondroitin sulfate has been shown to help rebuild the glycocalyx in animal models5.
• Nutraceuticals:
  • Endocalyx: Contains glucosamine (for heparan sulfate and hyaluronan synthesis), exogenous hyaluronan, fucoidan (heparan sulfate-like), and antioxidants. It is designed to maintain glycocalyx thickness and slow aging6.
  • Arterosil: Contains rhamnan sulfate, mimicking glycocalyx GAGs, and is intended to repair and restore glycocalyx structure6.
• Plasma and Platelet Transfusions: Used in trauma and hemorrhagic shock to help maintain glycocalyx integrity1.
• Pharmacological Agents:
  • Hydrocortisone: Reduces mast-cell degranulation and inflammation7.
  • Antithrombin III: Lowers susceptibility to enzymatic attack on the glycocalyx7.
  • TNF-alpha Inhibitors: Directly inhibit cytokine-mediated glycocalyx damage7.

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Emerging and Experimental Strategies

• Targeted Drug Delivery: Novel delivery systems are being developed to enhance the efficacy of glycocalyx regeneration therapies6.
• Balance of Heparanase Enzymes: Modulating the balance between heparanase-1 and heparanase-2 may attenuate injury in specific contexts (e.g., sepsis)1.
• Synthetic Polymers: Cationic copolymers that bind to the glycocalyx and improve endothelial barrier function are under investigation5.

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Summary Table: Key Interventions for Glycocalyx Support

Approach	Mechanism/Target	Evidence/Context
Normoglycemia, Euvolemia	Reduces shedding, maintains structure	Clinical recommendation5
Antioxidants	Scavenge free radicals	Experimental/clinical36
Albumin	Stabilizes endothelial surface	Clinical/experimental7
Glucocorticoids	Anti-inflammatory	Experimental/clinical37
Exogenous GAGs (e.g., HA, CS)	Rebuilds glycocalyx structure	Animal models5
Heparanase Inhibitors	Prevents enzymatic degradation	Experimental1
Nutraceuticals (Endocalyx, Arterosil)	Supports synthesis, mimics GAGs	Early human/animal data6
Plasma/Platelet Transfusion	Maintains integrity post-injury	Trauma/critical care1

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Conclusion
Effective maintenance and repair of the glycocalyx involve a combination of preventive measures (e.g., metabolic control, fluid management), antioxidants, targeted pharmacological agents, and emerging nutraceuticals and replacement therapies. While many interventions show promise in experimental models, further clinical research is needed to establish best practices for glycocalyx protection and restoration in humans1567.

1. https://pmc.ncbi.nlm.nih.gov/articles/PMC9923180/
2. https://www.sciencedirect.com/journal/matrix-biology-plus/special-issue/1060C86F4JK
3. https://www.sciencedirect.com/topics/medicine-and-dentistry/glycocalyx
4. https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1490395/full
5. https://journals.sagepub.com/doi/pdf/10.1177/0310057X1704500305
6. https://par.nsf.gov/servlets/purl/10324420
7. https://pubmed.ncbi.nlm.nih.gov/20462866/
8. https://www.orthomolecularproducts.com/product/RegeneVasc

Purely Nutraceutical Means to Support Glycocalyx Maintenance and Repair​

Excluding proprietary blends, several specific nutrients and dietary patterns have been identified in scientific literature as supportive of endothelial glycocalyx (eGC) health:
Key Nutraceuticals and Dietary Components

• Vitamin D
  Supplementation with vitamin D is associated with improved endothelial function and may help preserve the glycocalyx1.
• Omega-3 Fatty Acids
  Omega-3s, found in fatty fish and supplements, have anti-inflammatory effects and support vascular health, contributing to glycocalyx maintenance1.
• Polyphenols
  Plant-derived polyphenols such as resveratrol (grapes, red wine), quercetin (onions, apples), and catechins (green tea) exhibit antioxidant and anti-inflammatory properties that can protect the glycocalyx from oxidative damage and enzymatic degradation45.
• Dietary Nitrates
  Nitrate-rich vegetables (e.g., beets, spinach, arugula) enhance nitric oxide production, supporting vascular function and potentially protecting the glycocalyx14.
• Dietary Sulfur Compounds
  Foods like garlic and onions provide sulfur-containing compounds that may contribute to glycocalyx integrity14.
• Botanicals
  Some botanicals, such as rhamnan sulfate (from green seaweed), have demonstrated potential to support glycocalyx structure and function in animal and human studies5.
• Healthy Dietary Patterns
  • Mediterranean Diet: Emphasizes fruits, vegetables, nuts, olive oil, fish, and whole grains, which collectively support vascular health and glycocalyx preservation1.
  • Low-Carbohydrate Diets: Limiting high-glycemic and processed carbohydrates helps prevent glycocalyx damage caused by hyperglycemia23.
  • Potassium-Rich Foods: Fruits and vegetables high in potassium may help counteract the negative effects of dietary salt on the glycocalyx6.
• Intermittent Fasting/Time-Restricted Eating
  These eating patterns may support metabolic health and reduce risk factors associated with glycocalyx degradation1.

Summary Table: Purely Nutraceutical Approaches

Nutraceutical/Dietary Factor	Example Sources	Mechanism/Benefit
Vitamin D	Supplements, fortified foods	Endothelial protection
Omega-3 Fatty Acids	Fatty fish, flaxseed, chia	Anti-inflammatory, vascular support
Polyphenols	Berries, grapes, tea, apples	Antioxidant, anti-inflammatory
Dietary Nitrates	Beets, spinach, arugula	Nitric oxide production
Dietary Sulfur	Garlic, onions	Endothelial and glycocalyx support
Botanicals	Green tea, seaweed (rhamnan sulfate)	Antioxidant, structural support
Mediterranean Diet	Diverse plant-based foods, fish	Comprehensive vascular health
Low-Carb Diet	Meat, fish, non-starchy vegetables	Prevents hyperglycemia-induced damage
Potassium-Rich Foods	Bananas, leafy greens	Mitigates salt-induced damage
Intermittent Fasting	Structured eating windows	Metabolic and vascular benefits

These approaches are supported by emerging research and are distinct from proprietary blends, focusing instead on whole foods, specific nutrients, and dietary patterns1456.

1. https://pmc.ncbi.nlm.nih.gov/articles/PMC10255458/
2. https://www.naturecurefamilyhealth.com/keeping-your-glycocalyx-healthy/
3. https://www.doctorkiltz.com/glycocalyx/
4. https://www.kahnlongevitycenter.com/blog/loving-your-endothelium-and-the-glycocalyx
5. https://www.casi.org/node/1643
6. https://thepaleodiet.com/dietary-sa...e-risk-factor-you-may-never-have-heard-about/
7. https://pmc.ncbi.nlm.nih.gov/articles/PMC10592259/
8. https://www.mdpi.com/2072-6643/16/15/2572

Sorry for not placing it under a spoiler, but everyone should really know, since death by CVD is the most likely.

 

[SpacePenguin]

Glycocalyx is evident......

Thanks, pamojja! I didn't know about the glycocalyx, actually. But it seems like a lot of the advice for looking after it is generic advice about healthy diet and lifestyle. That makes me wonders if it's a central issue in CFS (maybe only downstream from high systemic inflammation).

 

[pamojja]

I'm even certain that systemic inflammation, is downstream of systemic dysfunction in many bodily systems, co-factored. And by above comprehensive means those co-factors also weaken.