They increase the risk of obesity. According to studies, industrial raised animals are given low doses of antibiotics to make them fatter, which could also occur in humans.
Can cause type I diabetes. Since antibiotics kill the beneficial bacteria in the intestines, they play havoc with your immune system. If you consume a large dose of them since an early age, it can cause your immune system to attack the pancreas, thus affecting your insulin-making process, causing diabetes.
They can destroy bacteria like H. pylori. Though a bad bacteria, it is the reason which protects people from asthma. Killing it can lead to asthma.
Resistant to infections. The biggest disadvantage of taking antibiotics on a regular basis is that it increases the risk of antibiotic resistant infections.