I call this "pruning a little." I recommend a daily mini-fast from 7 p.m. until your breakfast the next day to allow a little bit of your microbiome to "die off" each time. This is equivalent to trimming your microbiome so that it can continue to grow with the healthy probiotic bacteria that you'll be adding and nourishing.
You'll also want to include plenty of foods that have natural antimicrobial properties, especially herbs and spices such as garlic, ginger, and rosemary, and also coconut oil. And it’s really important to steer clear of (or minimize) foods that can harm your healthy gut bacteria and promote the growth of harmful microbes—including sugar, refined carbohydrates, food additives, pesticide-containing foods, and alcohol.
Finally, if you happen to notice that you feel worse after probiotic or prebiotic foods, you may have excessive levels of gut bacteria (a condition called small intestine bacterial overgrowth). In that case, it’s time to check in with your holistic practitioner for guidance.