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I’m not sure how accurate the passport analogy is. People get infected with (colonised by) foreign bacteria, parasites, viruses and fungi all the time. Faecal transplants don’t necessarily involve family members, and it’s unlikely even relatives have particularly similar gut flora, given the many variables involved in determining them. I think the right conditions make colonisation possible for the right species, but it’s not something I’ve researched, so correct me if I’m wrong.
I’ve been interested by some of the things Ayers says on his blog that have made me think the same things you’re thinking. I’m wondering if what he says about soil in particular is accurate.
Prof. Ayers wrote: To fix your gut flora, you need both proper food, and dozens of species of new bacteria. It is like a forest that is burned to clear it for a commercial plantation (wiping out gut flora with antibiotics). Adding more fertilizer will not cause the original complex forest to return. A source of seeds and plants representing the original biodiversity is needed to reproduce a functional forest. In the same way, repairing a damaged gut flora requires access to samples of the dozens, if not hundreds, of missing species of bacteria. Those needed bacteria are clinging to raw vegetables from local gardens, but are removed by excessive cleaning and sanitizing.