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cameroncowan comments on Open thread, Dec. 15 - Dec. 21, 2014 - Less Wrong
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People who have done paleo can sometimes have issues processes carbs because you lose the stomach bacteria necessary to do so. It was poorly phrased. The transition back can be hard.
Even then, it's not like you "lose the ability" -- the gut microbiota changes fairly rapidly so you should be fine in a few days. But I agree that transitions between very different restrictive diets can be hard on the body.
This runs contrary to what I've ready, but not specifically on gluten-related microbiota. Apparently change in the overall ecology of gut microbes can be very difficult to recover from.
Here is some data on the ease of changing one's microbiota. However you have a valid point in that the persistence of particular kinds of microbiota is not well understood and evidently it's possible to fall into, um, local minima that are hard to get out of (thus the whole fecal transplant business).
I suspect the reality here is much more complicated than the simple "easy to change"/"hard to change" approach.