Obesity, food and environmental allergies, heart disease and just about every other chronic health condition you can name is being linked to the health of the untold billions of viruses, bacteria and fungi that live inside you. The makeup of that biome has even been indicated in your food cravings.
Antibiotics are obviously decimating but that damage doesn't have to come in one fell swoop. Every time you eat food, that food then either feeds, starves or kills one kind of micro-organism in that biome that has so much influence on your life. The consumption of simple sugars and white breads feed bad microbes and rob good microbes of what they need to thrive. Eating meat contaminated with antibiotics obviously can have lessor but similar effects to just directly taking the antibiotics.
On top of your food, exercise also can have a dramatic effect. Getting that heart pumping distributes oxygen and nutrients around your body feeding both you and your biome. Athletes have been shown to have higher quantities of microbes that help maintain a healthy weight.