The brain-gut connection: Our "second brain" Your gut creates 95 percent of the serotonin in your body. That's why the brain and the gut have a lot in common, including the ways in which nerve cells talk with each other. Neurotransmitters are important chemicals that allow nerve cells to communicate. Serotonin is one of the most important neurotransmitters for that brain in your gut. Serotonin is important for the functions of your brain and your mood, but it is crucial to the function of your digestive system. Changes in your levels of serotonin and your sensitivity to serotonin signaling can change how your bowel works. A popular group of antidepressants, including Prozac, is called selective serotonin reuptake inhibitors (SSRIs). These drugs allow more serotonin to be available for your nerve cells to use. Everyone has a separate, mostly independent nervous system in their gut called the enteric nervous system. One hundred million nerve cells distributed throughout your digestive system direct movement through your intestines. This "second brain" can work independently of the one in your head, but there is an awful lot of talk back and forth between the two. Just think of butterflies in your stomach when you're nervous, or how anxiety can easily trigger your IBS cramps. What Does Serotonin Do? Serotonin affects many aspects of your gut function, including: It changes the motility of your bowels (how fast food moves through your system). It affects how much fluid, such as mucus, is secreted in your intestines. It affects how sensitive your intestines are to sensations like pain and fullness.