Taking nutritional supplements is a intentional choice that may have impact on my microbial communities. Supplements such as dietary fiber, may promote the growth of probiotics in our gut.
The choice of food we eat can have non-intentional impact on our microbial communities. For example, when we get travel to a foreign country, the local food we eat may break the balance of our gut communities, and make us get sick. Another example is that we happen to eat some food that was polluted by some harmful bacterial during the producing process. It is really dangerous if the bacterial get colonized in our gut since some bacterial are lethal.