The microbiome of bacteria in your gut is completely natural and helps your body to successfully function as a digestive agent. There are many ways to change the make up of the bacteria in your gut because they are living organisms that require certain factors in order to live. By changing these factors, you can change what bacteria are there.
To start, you can change your diet. Drastically changing the food that you eat will cause the bacteria in your gut to change as well since different organisms feed on different things. You can eat healthier food (less refined sugars and very processed meals) and add more vegetables (more fiber) to cause a healthy change in bacteria and improve your overall wellbeing. On the other hand, you could eat less healthy food and more processed meals with higher amounts of refined sugars to change the bacteria to ones that like more sugars. This would cause a negative affect on your health. Even small dietary changes like eating animal based foods or avoiding animal based foods will change the microbiome because certain bacteria can break down animal proteins while others do not.
You can also take vitamins and supplements to support the gut microbes that live in your gastrointestinal system. This will cause healthy growth of bacteria and decrease inflammation in the area. Overall, your health will improve with this because the bacteria will function better with the correct nutrients that they require.
There are also studies that show fermented foods will help your gut microbiome flourish. Often times, doctors will recommend this diet when you are on heavy antibiotics because the medication will deplete not only the bacteria that is causing your ailment, but it will also kill off the bacteria that is supposed to be in your body to aid it in daily functions, such as in your gut. By eating fermented foods such as yogurt, kombucha, or even fermented vegetables, your gut bacteria can replenish.
There are many ways to change the bacteria in your gut, but the most evidential way is to change your diet. This can be for the good of your bacterial colonies or for the worst; it all depends on what you eat.