The way that we do gut microbiome is using what's called metagenomics. This means you're sequencing all of the DNA in these microbes. So for example, you can look at how much it appears that your microbiomes might be making ammonia. The production of TMAO is 100% dependent on these on certain bacteria. If the bacteria aren't there, then you won't get TMA and it never becomes TMAO in your body and you don't have it.

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