I don't think you are right. There is actually quite a lot of literature demonstrating how species present in hunter-gatherers are not present in the guts of individuals from industrialized societies. See e.g. https://doi.org/10.1016/j.cell.2023.05.046.
Still, even if this was not the case at population level, my point would still hold. At individual level, many species are bimodal. With the wrong nutrients, infections, etc. your microbiome might fall into a state where you have none of them, as they have been outcompeted, and reversing that is incredibly difficult.
Still, even if this was not the case at population level, my point would still hold. At individual level, many species are bimodal. With the wrong nutrients, infections, etc. your microbiome might fall into a state where you have none of them, as they have been outcompeted, and reversing that is incredibly difficult.