Gut Feelings and Enteric Intelligence: The 100 Million Neurons in Your Belly That Make Decisions

Language: en

The Second Brain

There are 100 million neurons in your gut. One hundred million. That is more neurons than in the spinal cord. More than in the entire peripheral nervous system outside the gut. It is roughly the same number of neurons as in the brain of a cat.

This network — the enteric nervous system (ENS) — lines the walls of the gastrointestinal tract from esophagus to rectum, embedded in the tissue like a second brain wrapped around a long, winding tube. It can operate completely independently of the brain and spinal cord. If you sever all the nerves connecting the gut to the central nervous system, the gut continues to function — it continues to move food through the digestive tract, secrete enzymes, regulate blood flow, and coordinate the complex muscular contractions of peristalsis. No other organ system in the body can do this.

Michael Gershon, a neurobiologist at Columbia University and author of The Second Brain (1998), spent his career studying this enteric nervous system and arrived at a conclusion that was, at the time, radical: the gut is not just a digestive organ. It is a nervous system — a genuine information-processing network that receives input, processes it, generates output, and communicates its conclusions to the brain.

The folk wisdom knew this. Every language has expressions for it: “gut feeling,” “butterflies in the stomach,” “gut instinct,” “I feel it in my gut,” “gutsy,” “gut-wrenching.” These are not metaphors. They are reports of a real physiological phenomenon — the enteric nervous system generating information that reaches consciousness as a felt sensation in the abdomen.

The Architecture of Enteric Intelligence

The Enteric Nervous System

The ENS is organized into two layers:

The myenteric plexus (Auerbach’s plexus). Located between the longitudinal and circular muscle layers of the gut wall, this network controls gut motility — the muscular contractions that move food through the digestive tract. It contains motor neurons, interneurons, and sensory neurons organized into circuits that can independently coordinate the complex patterns of contraction and relaxation required for peristalsis.

The submucosal plexus (Meissner’s plexus). Located in the submucosa (the layer beneath the gut lining), this network controls secretion (enzyme production, mucus production, ion transport) and blood flow to the gut lining. It responds to the chemical composition of the gut contents and to signals from the gut microbiome.

These two networks contain a full complement of neuron types:

• Sensory neurons that detect mechanical stretch, chemical composition, pH, temperature, and the presence of nutrients, pathogens, and microbial metabolites
• Interneurons that process this information and relay it within the enteric network
• Motor neurons that control muscle contraction, secretion, and blood flow
• Glial cells (enteric glia) that support neuronal function and participate in immune defense

The ENS uses more than 30 neurotransmitters — essentially the same neurotransmitter repertoire as the brain. Notably:

Serotonin (5-HT). Approximately 95% of the body’s serotonin is produced in the gut — not in the brain. Gut serotonin is produced by enterochromaffin cells in the gut lining and by enteric neurons. It regulates motility, secretion, and gut sensation, and it communicates with the brain via the vagus nerve.

Dopamine. Approximately 50% of the body’s dopamine is produced in the gut. Gut dopamine influences motility and mucosal blood flow.

GABA. The gut produces significant quantities of GABA, the brain’s primary inhibitory neurotransmitter. Gut GABA influences enteric neuron activity and communicates with the brain via the vagus nerve.

Acetylcholine, substance P, nitric oxide, vasoactive intestinal peptide (VIP), and neuropeptide Y — all major signaling molecules of the brain — are also produced and used by the enteric nervous system.

The Gut-Brain Axis

The ENS communicates with the brain through multiple pathways:

The vagus nerve. The primary neural highway between the gut and the brain. Approximately 80% of vagal fibers are afferent (carrying information from gut to brain), making the vagus primarily a sensory nerve that reports gut state to the brainstem, which then relays the information to the insula, amygdala, hypothalamus, and prefrontal cortex.

The vagus carries information about: gut distension (fullness), nutrient composition (what you ate), inflammatory state (immune activation in the gut), microbial metabolites (what the bacteria are producing), and emotional gut responses (the contractions, secretions, and blood flow changes that accompany emotional states).

Spinal afferent neurons. Sensory neurons in the gut wall project through the spinal cord to the brain, carrying primarily pain and distension signals. These are the pathways responsible for visceral pain (stomach ache, intestinal cramping) and for the sensation of extreme gut distress.

Hormonal signaling. The gut produces hormones (ghrelin, leptin, cholecystokinin, peptide YY, glucagon-like peptide-1) that enter the bloodstream and reach the brain, influencing appetite, satiety, mood, and cognitive function.

Immune signaling. The gut contains approximately 70% of the body’s immune cells. Immune activation in the gut produces cytokines (TNF-alpha, IL-1-beta, IL-6) that can cross the blood-brain barrier and influence brain function — this is the mechanism through which gut inflammation can cause brain fog, depression, and cognitive impairment.

Microbial metabolites. The gut microbiome produces a variety of neuroactive compounds (short-chain fatty acids, tryptophan metabolites, secondary bile acids) that reach the brain via the bloodstream or the vagus nerve and directly influence neural function.

Gut Feelings: The Science of Visceral Intuition

How the Gut Generates Decision-Relevant Information

The gut responds to emotional stimuli faster than conscious awareness can process them. When you encounter a situation that your past experience has marked as dangerous, rewarding, or otherwise significant, the following sequence occurs:

1. The amygdala detects the emotional significance of the situation (often before conscious awareness).
2. The amygdala sends signals via the autonomic nervous system to the gut.
3. The gut responds: smooth muscle contracts or relaxes, blood flow changes, secretory activity shifts, the enteric nervous system generates a specific pattern of activity.
4. These gut changes produce sensations: tightness, butterflies, sinking, warmth, opening, churning.
5. These sensations travel via the vagus nerve to the brainstem and then to the insula, where they are integrated into conscious awareness as “gut feelings.”

The entire sequence — from stimulus detection to gut response to conscious gut feeling — occurs in approximately 200-500 milliseconds. The gut feeling arrives in consciousness before the analytical mind has had time to evaluate the situation logically.

This is why gut feelings feel like they arrive “from nowhere” — they are the output of a rapid, automatic, body-based evaluation system that operates faster than conscious reasoning.

Emeran Mayer’s Research

Emeran Mayer, a gastroenterologist at UCLA and author of The Mind-Gut Connection (2016), has conducted extensive research on the bidirectional communication between the gut and the brain and its implications for emotion and decision-making.

Mayer’s key findings include:

Gut microbiome composition affects emotional processing. Using fMRI, Mayer showed that women who consumed a probiotic-containing fermented milk product for four weeks showed altered brain responses to emotional stimuli — specifically, reduced reactivity in the insula and somatosensory cortex to images of negative emotional faces (Tillisch et al., 2013, published in Gastroenterology). Changing the gut bacteria changed the brain’s emotional processing.

Gut inflammation alters brain function. In patients with irritable bowel syndrome (IBS), Mayer demonstrated that gut inflammation is associated with altered activity in brain regions involved in emotional processing, interoception, and pain — the insula, anterior cingulate cortex, and amygdala. The inflamed gut sends amplified alarm signals to the brain, producing anxiety, hypervigilance, and altered emotional processing.

The gut microbiome influences stress reactivity. Germ-free mice (raised without any gut bacteria) show exaggerated stress responses — elevated cortisol, increased anxiety-like behavior — compared to mice with normal gut bacteria. Colonizing germ-free mice with normal gut bacteria normalizes their stress response. This demonstrates that the gut microbiome is required for normal stress regulation — it is not just a passive passenger but an active participant in the body’s stress response system.

John Cryan’s Psychobiotic Research

John Cryan at University College Cork (APC Microbiome Ireland) has been at the forefront of research on the gut microbiome’s influence on brain and behavior — a field he helped name “psychobiotics.”

Lactobacillus rhamnosus and anxiety. Bravo et al. (2011), in a landmark study published in Proceedings of the National Academy of Sciences, showed that feeding mice the probiotic bacterium Lactobacillus rhamnosus (JB-1) reduced anxiety-like and depression-like behaviors and altered GABA receptor expression in the brain. Critically, these effects were abolished by vagotomy — cutting the vagus nerve. This proved that the bacterial signals were reaching the brain specifically through the vagal pathway.

Microbiome and social behavior. Desbonnet et al. (2014) showed that germ-free mice have significant social behavior deficits — they show reduced social motivation, impaired social recognition, and altered social cognition. Colonization with normal gut bacteria during early life partially restores normal social behavior. This suggests that the gut microbiome is required for normal social brain development.

Microbiome and stress resilience. Cryan’s group has shown that specific bacterial strains (including Bifidobacterium longum and Lactobacillus rhamnosus) can reduce cortisol responses to stress, improve cognitive performance under stress, and alter the expression of stress-related genes in the brain — all through gut-to-brain signaling.

The Microbiome as Decision-Making Influence

How Bacteria Shape Your Choices

The gut microbiome — the 38 trillion bacteria that inhabit your digestive tract — influences brain function through multiple mechanisms:

Short-chain fatty acid (SCFA) production. Gut bacteria ferment dietary fiber into SCFAs (primarily butyrate, propionate, and acetate). These molecules:

• Cross the blood-brain barrier and directly influence neural function
• Activate vagal afferent neurons, sending signals to the brain
• Modulate immune function (reducing inflammation)
• Influence the production of neurotransmitters (serotonin, GABA, dopamine) by enteric cells

Tryptophan metabolism. The gut microbiome modulates the availability of tryptophan — the amino acid precursor of serotonin. Some bacteria consume tryptophan (reducing its availability for serotonin production), while others produce tryptophan metabolites that have their own neuroactive effects. The composition of your gut microbiome literally determines how much serotonin your body can produce.

Vagal nerve signaling. Specific bacterial species activate vagal afferent neurons, sending signals directly to the brain. Different bacterial compositions produce different patterns of vagal signaling — and thus different patterns of brain activation.

The implication is remarkable: your gut bacteria are not passive residents. They are active participants in the generation of the body signals that influence your emotions, your stress responses, and your decisions. When you have a gut feeling, part of that feeling is generated by bacterial metabolites acting on enteric neurons and vagal afferents.

Your gut feeling is, in a very real sense, partly a bacterial feeling.

The Dietary Connection

This creates a striking causal chain: what you eat determines which bacteria thrive in your gut. The bacteria produce metabolites that influence your brain chemistry. Your brain chemistry influences your emotions, thoughts, and decisions. Therefore: your diet influences your decision-making — not just through blood sugar effects or nutritional status, but through the gut microbiome’s modulation of the brain.

High-fiber plant-based diets promote bacterial diversity and SCFA production — supporting a gut-brain axis that favors calm, clear emotional processing and effective decision-making.

High-sugar, high-fat, low-fiber diets promote bacterial compositions associated with inflammation, reduced SCFA production, and altered neurotransmitter balance — supporting a gut-brain axis that favors anxiety, emotional reactivity, and impaired decision-making.

The functional medicine approach to gut health — removing inflammatory foods, restoring beneficial bacteria through probiotics and fermented foods, reinoculating with diverse plant fibers, and repairing the gut lining — is, from this perspective, not just a digestive intervention. It is a consciousness intervention. It optimizes the gut-brain axis that generates the somatic markers, gut feelings, and interoceptive signals that guide emotional processing and decision-making.

The Gut as Consciousness Organ

Beyond Decision-Making

The gut’s contribution to consciousness extends beyond decision-making:

Mood regulation. Given that 95% of serotonin is produced in the gut, and that serotonin profoundly influences mood, the gut is a major determinant of emotional tone. Gut inflammation, dysbiosis (microbial imbalance), and altered gut serotonin production are associated with depression, anxiety, and emotional dysregulation.

Immune-mediated consciousness changes. The gut’s role as the body’s largest immune organ means that gut immune activation directly affects brain function. The fatigue, brain fog, and mood changes of “sickness behavior” are mediated by cytokines produced in the gut reaching the brain. Chronic, low-grade gut inflammation — increasingly common in industrialized populations due to diet, stress, and environmental exposures — may be contributing to the epidemic of cognitive and emotional difficulties in modern life.

Interoceptive contribution to self-awareness. The gut generates a substantial portion of the interoceptive signal that reaches the insula — the brain region that Bud Craig has identified as the generator of subjective self-awareness. The gut’s contribution to the interoceptive stream (sensations of hunger, fullness, comfort, discomfort, butterflies, sinking feelings) is a major component of the felt sense of being alive.

Sleep and circadian regulation. The gut microbiome has its own circadian rhythms, and these rhythms influence the production of melatonin (the gut produces 400 times more melatonin than the pineal gland), serotonin, and other neuroactive compounds that affect sleep quality and circadian consciousness states.

Indigenous and Traditional Knowledge

The Belly as Wisdom Center

Many indigenous and traditional healing systems place the belly — not the head — at the center of wisdom and knowing:

The Japanese hara. In Japanese culture, the hara (belly, specifically the lower abdomen) is considered the center of vital energy, intuition, and authentic action. The expressions “haragei” (the art of the belly — communication through unspoken understanding) and “harakiri” (cutting the belly — the most honorable form of death, because it opens the center of the self) reflect this cultural understanding.

The Chinese dantian. In Chinese medicine and Taoist practice, the lower dantian (located approximately three finger-widths below the navel) is considered the body’s primary energy center — the origin point of qi and the seat of embodied wisdom. Taoist meditation practices focus on the dantian as the starting point for energy cultivation.

Ayurvedic agni. In Ayurvedic medicine, agni (digestive fire) is considered the foundation of health and consciousness. The state of the digestive system determines the clarity of the mind — a principle now supported by gut-brain axis research.

Indigenous gut knowing. Many indigenous cultures describe a knowing that comes from the belly — distinct from the knowing of the head. Aboriginal Australian traditions include the concept of knowledge that resides in the gut and that communicates through physical sensation. Amazonian healing traditions use dietas (restrictive dietary practices) to sensitize gut awareness as a diagnostic tool.

These traditions converge on a recognition that the gut is not merely a digestive organ but a knowing organ — a center of intelligence that communicates through sensation and that provides information about the world that the analytical mind cannot access.

Practical Applications

Developing Gut Intelligence

Based on the research, developing gut-based intelligence involves both optimizing the gut’s information-generating capacity and enhancing the brain’s ability to receive and process gut signals:

Optimize the gut environment. Feed the microbiome a diverse, fiber-rich, plant-forward diet. Include fermented foods (kimchi, sauerkraut, kefir, yogurt). Minimize processed foods, artificial sweeteners, and unnecessary antibiotics. Address gut infections and inflammation through functional medicine testing and treatment.

Develop gut awareness. Practice noticing gut sensations throughout the day — before meals, after meals, during emotional experiences, before decisions. The gut is constantly signaling; the challenge is learning to detect and interpret those signals.

Gut-feeling journaling. Before significant decisions, note the gut’s response. After decisions, note the outcome. Over time, patterns emerge that reveal the accuracy and character of your gut intelligence.

Breath-gut connection. Deep, slow diaphragmatic breathing massages the abdominal organs and stimulates the vagus nerve — enhancing both gut function and gut-to-brain communication. The practice of breathing into the belly is not just a relaxation technique; it is a way of activating and listening to the enteric nervous system.

Reduce gut-masking behaviors. Chronic stress, emotional eating, alcohol, and excessive caffeine all alter gut signaling in ways that obscure the gut’s natural intelligence. Reducing these behaviors allows the gut’s baseline signals to become more clear and more detectable.

The gut is a brain. It contains 100 million neurons, produces most of the body’s serotonin and dopamine, houses 70% of the immune system, and communicates continuously with the brain via the vagus nerve, the immune system, and microbial metabolites. It generates information about the body’s state, the emotional significance of situations, and the quality of the food and microbial environment that it processes.

When you say “I had a gut feeling,” you are not being metaphorical. You are reporting the output of a genuine nervous system — a second brain that has been generating intelligence for every moment of your life, whether or not you have been listening.

The 100 million neurons in your belly are not waiting for instructions from your head. They are generating their own assessment of the world — and that assessment, when it reaches your consciousness as a felt sensation in your abdomen, is one of the most valuable sources of intelligence you possess.

Learn to listen.