Serotonin is widely known as a brain neurotransmitter linked to mood, sleep and appetite. Yet an often overlooked fact is that about 90% of the body’s serotonin is synthesized in the gastrointestinal tract. This article summarizes the physiology, gut–brain connections, and practical factors that influence gut-derived serotonin. What is gut serotonin? Serotonin (5‑HT) is made from the essential amino acid tryptophan via 5‑HTP. In the gut, specialized enterochromaffin cells produce the majority of peripheral serotonin, which acts locally on the enteric nervous system and immune cells. Gut serotonin regulates motility, visceral sensitivity, and contributes to immune signaling, but it does not cross the blood–brain barrier; central and peripheral serotonin pools are largely separate. Gut–brain communication The enteric nervous system (ENS), sometimes called the “second brain,” contains millions of neurons that interact with serotonin, the vagus nerve, and circulating metabolites. Microbial metabolites such as short‑chain fatty acids and other signals modulate enterochromaffin activity and tryptophan availability. For a focused discussion on enterochromaffin function and serotonin production, see [Serotonin produced in the gut](https://www.innerbuddies.com/blogs/gut-health/serotonin-produced-in-gut). Microbiome influence and clinical relevance Gut microbes influence serotonin through multiple pathways: stimulating enterochromaffin cells, altering tryptophan metabolism, and modifying local inflammation that shifts tryptophan toward the kynurenine pathway. Specific bacterial strains (for example, some Bifidobacterium and Lactobacillus species) have been associated with changes in gut‑derived serotonin and related behaviors in preclinical and early clinical studies. Clinically, dysregulated gut serotonin has been implicated in conditions such as irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), small intestinal bacterial overgrowth (SIBO), and may contribute indirectly to mood disorders through gut–brain axis mechanisms. For practical approaches to microbiome assessment and how testing differs for consumers and healthcare professionals, see gut microbiome testing differences. For connections between gut composition and athletic performance, refer to gut microbiome and endurance. Supporting healthy gut serotonin Evidence‑based factors that influence peripheral serotonin include diet, inflammation control, sleep, exercise, stress management, and microbial diversity. Dietary tryptophan is necessary but not sufficient; vitamin cofactors (B6, B3, iron), competitive amino acid transport, and microbiome composition all affect conversion. Regular aerobic exercise and sleep hygiene support serotonin and melatonin balance. Managing chronic inflammation helps preserve tryptophan availability for serotonin rather than diversion to neuroactive kynurenines. For those exploring diagnostic options, product and testing information is available (e.g., microbiome test). Conclusion Recognizing that most peripheral serotonin is produced in the gut reframes how we think about mood, digestion, and immunity. Integrating dietary, lifestyle, and microbiome‑focused strategies supports the metabolic pathways that generate gut serotonin, which in turn affects motility, immune signaling, and communication along the gut–brain axis. Understanding these links can inform research and clinical approaches to disorders where gut and brain interact.