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).