Answer by Tanush Jagdish:
This is a wonderful and forward-looking question.
Ecological techniques can in general be applied to look at microbiota-host relationship.
In some ways, maintaining a healthy microbiota is like lawn care: severe interventions can take the ecosystem back to bare earth, so it has to be re-established. Although many people recover naturally, this is not guaranteed, and weed-like species that are adapted to perturbed ecosystems often run wild.
Several strategies can be used to restore the ecosystem: reseeding with a few well-defined ‘good’ microbes (probiotics), adding compounds that are thought to specifically promote the growth of beneficial microbes (prebiotics) and transplanting the entire microbial ecosystem, for example from a stool sample (faecal bacteriotherapy).
The weed stage could be bypassed by administering the treatment immediately after the disturbance before the weeds can establish themselves. An additional strategy (not shown) is to use specific drugs, such as narrow-spectrum antibiotics, that target undesirable members of the microbial community. Although we are beginning to learn what a healthy microbial community looks like, and to recognize signs of weed species, our understanding of which strategies for altering the microbiota work best, and predicting which will work for a given individual, is still in its infancy.
But to answer you question specifically, we don’t have an answer. Two reasons:
1. While we know differential diets change gut microbial diversity and abundance, we don’t how. And while we know that stable microbiota equilibrium is reacquired given enough time to stabilize, yeah, you guessed it – we don’t know how.
2. Even if we had a general idea how, we wouldn’t know how it works for you. Microbiota responses are highly individualized. For instance, here’s snippet from a study with ciprofloxacin:
However, the magnitude of disturbance that occurred after ciprofloxacin treatment, and the speed and extent of recovery to the pre-ciprofloxacin state, suggested that resilience of the microbiota varies across individuals and between ciprofloxacin treatments in the same individual.