A healthy microbiome can help to regulate the bacteria in other parts of your body, like your skin. According to Joshua Zeichner, M.D., a dermatologist with Mount Sinai Hospital in New York City, an unbalanced gut microbiome can cause inflammation that affects the entire body, including your skin, which can lead to breakouts. One study found that 54 percent of patients with acne had impaired microbiomes compared to those of the average person.