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.

Lozupone et. al.

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.
(Page on nature.com)

How can I manipulate gut flora?

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