Microbiome - Butyrate - Inflammation

[Wayne]

ChatGPT reckoned that NAC was inadvisable

Hi @SpacePenguin -- Thanks for the informative post. Also want to mentioned that I'm appreciating your comments about how you're using ChatGPT. It's such a valuable resource for us, and yet I think too many are reluctant to use it. Maybe because of unfamiliarity, or perhaps a bit intimidated by learning a new skill.

I will say, learning how to best use it does seem to be a skill that doesn't just happen overnight. But the more we learn about its capabilities, its strengths, its weaknesses, the more we can take advantage of it. Not only for health research, but to make our everyday lives much more manageable and easier.

 

[pamojja]

Interesting sidenote: apparently only shotgun metagenomics can distinguish amongst the species and strains of akkermansia. 16s tests will just give a result for Akkermansia as a whole genus, in which case you would not know whether you had potentially problematic non-muciniphila taxa.

In my ubiome result it showed 0.21 percent akkermansia genus, but 0.19% akkermansia muciniphilia.

Spoiler: genus vs. specie

Your observation that your uBiome report listed both "Akkermansia genus" and "Akkermansia muciniphila" with specific percentages is notable. While 16S rRNA sequencing (the technology used by uBiome) generally has limited resolution and often cannot reliably distinguish between closely related species or strains, there are exceptions:

• Some regions of the 16S rRNA gene contain enough variability to allow identification of certain species, especially if that species is the only well-characterized member of its genus in human gut samples. Akkermansia muciniphila is currently the dominant—and in many cases, the only—recognized species of Akkermansia commonly found in the human gut4.
• Because of this, some 16S pipelines will report both the genus and the most likely species (e.g., Akkermansia muciniphila) when the sequence matches closely enough, but this is an inference rather than a definitive species-level identification24.
• The percentages you saw reflect the relative abundance as estimated by 16S sequencing, but this does not mean the test could distinguish between multiple Akkermansia species or strains. If another Akkermansia species were present, the test likely would not have detected or differentiated it.

In summary, while your uBiome report included both genus and species-level results for Akkermansia, this was based on the limitations and assumptions of 16S rRNA sequencing, which cannot reliably distinguish between all species or strains within a genus. The presence of Akkermansia muciniphila was likely inferred because it is the predominant species, not because the test could definitively distinguish it from all possible Akkermansia species or strains24.

1. https://newsnetwork.mayoclinic.org/...-measures-health-of-a-persons-gut-microbiome/
2. https://pmc.ncbi.nlm.nih.gov/articles/PMC8206793/
3. https://www.statnews.com/2024/01/02/microbiome-gut-tests-at-home-digestive-health/
4. https://pmc.ncbi.nlm.nih.gov/articles/PMC6052657/
5. https://sifted.eu/articles/do-microbiome-tests-work
6. https://www.medicalnewstoday.com/articles/microbiome-testing
7. https://www.nytimes.com/2021/10/13/well/live/microbiome-test.html
8. https://www.nbcnews.com/health/heal...prove-gut-health-science-isn-t-solid-n1277196

Wow.

 

[SpacePenguin]

Hi @SpacePenguin -- Thanks for the informative post. Also want to mentioned that I'm appreciating your comments about how you're using ChatGPT.

Thanks, Wayne! I was surprised that I hadn't seen anyone doing this with their gut microbiome tests, which is why I posted about it. I like to treat ChatGPT as a slightly goofy collaborator - goofy because it sometimes makes dumb mistakes (especially when doing maths) and has an odd upbeat tone. So I have long conversations: asking it what it by this and that, how sure it, what is it's evidence, how it can reconcile things it has said that seem to conflict, even ask it how I should use it and what I should ask.

It's such a valuable resource for us, and yet I think too many are reluctant to use it. Maybe because of unfamiliarity, or perhaps a bit intimidated by learning a new skill.

Some of the expressions of caution I have heard from people are overblown in my view. There have been at least three doctors that have given me terrible advice that has damaged me (perhaps even seriously and long-term). GenAI can be a great supplement to care from a human doctor - it has access to vastly data and informational analysis than a human, but the human has perception, judgment, and personal interaction.

I will say, learning how to best use it does seem to be a skill that doesn't just happen overnight. But the more we learn about its capabilities, its strengths, its weaknesses, the more we can take advantage of it. Not only for health research, but to make our everyday lives much more manageable and easier.

Absolutely! Like all tools, it requires skill. You can use it well or poorly. And you can always improve the way you use it (especially in terms of writing prompts).

 

[SpacePenguin]

....16S rRNA sequencing, which cannot reliably distinguish between all species or strains within a genus. The presence of Akkermansia muciniphila was likely inferred because it is the predominant species, not because the test could definitively distinguish it from all possible Akkermansia species or strains....

Hmmm, so maybe they assumed that ratio of muciniphila to non-muciniphila simply based on expected/average results (which presumably they would have needed shotgun metagenomics to determine).

 

[LINE]

I am wrapping up this thread since interest is no longer.

I did some more deep dives on the microbiome and continued experiments which I will outline below:

1/ The intestinal tract is more diverse than most know - there is a host of interactions that not only occur solely in the gut but also throughout the entire body. It is clear in the medical research that the GI tract affects stool but is intimately tied to neurological, immune and endocrinological responses.

2/ The microbiome is certainly a major player, and it affects systems like barrier integrity which is a critical element. The microbiome can change under immune stress caused by pathogens which could include viral responses but also bacterial, yeast or parasitic challenges. Environmental toxins are another challenge that the microbiome must face. With these challenges, the environment is impacted which can cause more chaos.

3/ There are a number of factors in the gut experience which include the microbiome, but other factors are there including barrier integrity (tight junction proteins which was the start of this thread (butyrate), and there are quite a few signaling pathways such as GPX2, mTOR, AMPK and others. Just like there are many components to an engine, there are many in the gut and they have dependency on each other. Crosstalk would be a good word to use.

The point I am trying to make is that there is complexity which requires experimentation. I have made progress, albeit slow by addressing multiple things, it has been a lot of work. The GI system should not be overlooked as I feel it is the place that has most importance. Thank you all for participating.

Tags: NAG, fermented foods, resistant starch, Vitamin A, Vitamin D, butyrate, magnolia, caprylic acid, quercetin, neem, zinc carnosine, benfotiamine, binders, bile acids, selenium, NKO oil, polyphenols, natural antimicrobials,

 

[Wayne]

Environmental toxins are another challenge that the microbiome must face.

I tend to believe that environmental toxins play a far greater role in compromised health that most people ever consider. I just ran across information recently on PFAS which has me thinking about eating oatmeal more frequently. I really feel I need to set up a regimen of incorporating other binders like charcoal and bentonite clay on a daily basis to "mop up" much of what doesn't belong in our GI tract.

Oat bran, specifically the beta-glucan soluble fiber it contains, has been found to help reduce and detoxify PFAS (per- and polyfluoroalkyl substances, also known as forever chemicals) in the gastrointestinal tract. Beta-glucan forms a gel-like substance in the gut that binds to PFAS and bile acids, preventing their reabsorption into the bloodstream and facilitating their excretion in feces. This effect has been demonstrated in both animal studies and human clinical research, showing reduced blood levels of certain PFAS compounds after oat beta-glucan supplementation.​

 

[pamojja]

has me thinking about eating oatmeal more frequently.

Oatmeal might not be optimal for prediabetics (like me). For example, a 40 g serving only contains 1.8 g beta-glucan. 24 g oat bran I use has that much beta-glucan too.

 

[Wishful]

The GI system should not be overlooked as I feel it is the place that has most importance.

I agree that it's an important place for experimentation. The brain might be more important in terms of ME, but it's so much harder and riskier to experiment with modifying that. Achieving an improvement in ME can take as little as adding or avoiding one food.

The point I am trying to make is that there is complexity which requires experimentation.

Yes, and it likely requires continual experimentation, because the responses to foods change, sometime gradually, and sometime abruptly. There might be some PWME for whom every morning is a fresh start in trying to figure out what is safe to eat.

 

[Wishful]

has me thinking about eating oatmeal more frequently.

Oats are a significant portion of my daily food intake, but I haven't felt that it's made any significant improvements in my ME (by binding toxins or whatever). I like oats, and judge them a healthier option than wheat flour.

 

[Rufous McKinney]

Excellent Thread, I'd like to wade through more of the great info you've posted, @LINE. And a nice thread title, maybe I can in fact find it again.