Antibiotics could cause a change in the gut microbial community by killing certain microbes. This would cause a change in the composition of the community. In some situations, this could be beneficial (as in the case of an infection), but often, beneficial microbes are killed in the process, leading to a detrimental effect on human health.
Changing one’s diet could also greatly alter a person’s microbiome composition. For example, someone who has been a strict vegan for a long period of time may have an altered microbiome that is not accustomed to eating animal products. Digesting meat could be very difficult for them until the gut microbial composition is able to adjust to the change in diet. Changing diet could either have a beneficial or detrimental effect, depending both on the type of change in diet and the particular person’s microbiota.
Taking a probiotic could change the gut microbial community by introducing different microbes to the host’s digestive system, which often has a beneficial effect, especially after a round of antibiotics.
Taking a prebiotic would help feed beneficial bacteria that already inhabit a person’s gut, which would have either a beneficial or neutral effect on one’s gut microbial community. Prebiotics may help increase the number of “good bacteria” within a person’s gut by offering them additional nutrients.