The Gut–Brain Axis: How Digestive Health Shapes Mental Health

Up to 60% of adults experience digestive complaints, and emerging research shows that gut dysfunction is closely tied to mental health challenges like low mood, anxiety, and brain fog (Clapp et al., 2017; Kelly et al., 2016). Even without overt digestive symptoms, gut health may still be compromised such that dysfunction in the brain and body still occurs. Yet many people chalk these symptoms up to “stress” or “just a bad day,” overlooking the profound ways digestive health influences brain function.

Even with good nutrition, regular activity, and sufficient sleep, irritability, brain fog, or mood fluctuations may indicate imbalances in the gut–brain axis—the bidirectional communication network connecting the digestive system, the enteric nervous system (part of the peripheral nervous system), and the central nervous system.

Beyond “It’s All in Your Head”

For decades, mental health has been framed almost exclusively in terms of neurotransmitters like serotonin, dopamine, and GABA. But research now paints a richer picture: gut microbial balance, immune signaling, digestive function, and food sensitivities are integral to mood and cognition. Mental health isn’t just about “too little serotonin.” It’s the story of how your gut, immune system, and brain communicate—or fail to communicate—in harmony.

The gut–brain axis refers to the constant, bidirectional communication between the gastrointestinal tract and the nervous system. This network links the enteric nervous system (ENS)—sometimes called the “second brain”—with the central nervous system (CNS) through neural, hormonal, and immune pathways (Carabotti et al., 2015). A central player is the vagus nerve, which carries signals from the gut to the brain about digestion, microbial activity, and inflammation, while also transmitting calming parasympathetic input from the brain back to the gut.

When the gut is balanced, this system supports mood regulation, stress resilience, and cognitive clarity. But when gut function is compromised—through dysbiosis, inflammation, or barrier disruption—this communication becomes distorted. Signals of distress from the gut can amplify stress responses in the brain, disrupt neurotransmitter balance, and contribute to anxiety, low mood, or brain fog (Foster et al., 2017).

Microbial Imbalances and Mood

● Up to 50–60% of people with depression show altered gut microbiota composition and reduced SCFA production (Clapp et al., 2017; Kelly et al., 2016).

● Elevated LPS and pro-inflammatory cytokines correlate with low mood, anxiety, and cognitive decline (Maes et al., 2008).

Digestive Dysfunction

● Functional dyspepsia, SIBO, and chronic gut infections affect 30–40% of adults experiencing persistent brain fog or mood fluctuations (Quigley, 2011).

● Hypochlorhydria and pancreatic insufficiency reduce amino acid absorption, limiting precursors for serotonin, dopamine, and norepinephrine.

How the Gut Shapes the Brain

Food sensitivities

Even mild, chronic reactions, can drive immune activation, low-grade inflammation, and subtle cognitive or mood disturbances. Identifying and managing these sensitivities can relieve fatigue, brain fog, and emotional instability.

LPS and Systemic InflammationLeaky gut allows LPS and other microbial products into the bloodstream, triggering immune activation and cytokine release. Chronic inflammation disrupts neurotransmitter pathways and may manifest as low mood, irritability, or mental fatigue.

SCFAs: Microbial Metabolites That Support Brain Health

SCFAs like butyrate, acetate, and propionate feed colon cells, strengthen the gut barrier, and regulate immune responses. They also support neurotransmitter production and stress resilience.

Cytokines and NeurotransmittersExcess pro-inflammatory cytokines (IL-6, TNF-alpha) interfere with dopamine and serotonin pathways, reduce neurogenesis, and amplify stress responses. Gut dysbiosis often drives this inflammatory environment.

Digestive Enzymes & Stomach AcidLow stomach acid or pancreatic enzyme insufficiency impairs protein digestion, limiting essential amino acids needed for neurotransmitter synthesis. Over time, this can contribute to brain fog, low motivation, and mood instability.

Dysbiosis & Chronic InfectionsImbalanced gut microbes or persistent infections like Candida, H. pylori, or SIBO reduce nutrient absorption, increase oxidative stress, and fuel inflammation—factors that impact both hormone and neurotransmitter balance.

Structural Changes in the GutBlunted brush border, crypt hyperplasia, and SIgA imbalances affect nutrient absorption, gut barrier integrity, and immune regulation, contributing to cognitive and emotional symptoms.

Metabolic EndotoxemiaElevated circulating bacterial endotoxins from gut dysfunction increase systemic inflammation, impacting mood, motivation, and resilience.

Persistent low mood and stress can be destabilizing and its sources hard to parcel out. Currently we mistake symptoms as causes but the influence of the gut, diet, and lifestyle as implicated above, shows that the root causes may actually be below (the brain). Addressing gut health can be a path toward transforming one’s life. Our habits, environment, levels of stress and what we consume all have pronounced effects. Supporting the gut becomes about more than just “fixing” digestion—it can help restore energy, immunity, mood stability, mental clarity and more.

What You Can Do at Home Today

● Support gut barrier integrity: Fiber-rich vegetables, prebiotic foods, and fermented, or probiotic rich foods.

● Reduce pro-inflammatory triggers: Limit ultra-processed foods, refined sugars, and alcohol.

● Identify and manage food sensitivities: Elimination or rotation diets can reduce immune activation and improve mood.

● Manage stress: Meditation, breathwork, and gentle movement support gut-brain communication.

● Optimize digestion: Ensure adequate stomach acid, digestive enzymes, and bile flow.

● Basic nutrient support: Multivitamin, omega 3s, magnesium.

○ Probiotics, ACV, enzymes, HCL, bile acids and the like can be very helpful…if needed and indicated. Actually knowing if they are or not is almost impossible without testing though.

Why Guesswork Can Backfire

The gut microbiome is highly individualized and it’s almost impossible to guess the exact state of it. For example, a person may have toe fungus but no Candida overgrowth in the GI tract, which changes the appropriate protocols. It would make sense to guess they have candida in the gut, but they may not so the protocol changes. A candida protocol could disrupt microbial balance in the GI in this instance. Similarly, someone may have have SIBO, which requires a careful, targeted approach to probiotics or antimicrobials. Simply guessing and taking more probiotics of particular strains like Lactobacillus and Bifidobacterium which may normally be helpful and healthy can actually exacerbate symptoms if interventions aren’t aligned with the underlying imbalance. Due to the fundamental importance of microbial and digestive health, and how difficult it is to guess, testing should be a high priority whenever possible.

How We Can Help

If mood, focus, or cognitive clarity feel off despite your best efforts, it may be time to explore the gut-brain connection. At Seed to Fruit, we offer functional assessments to uncover hidden digestive and microbial imbalances:

● Comprehensive GI panels → detect dysbiosis, infections, and inflammatory markers.

● Intestinal permeability testing → reveals gut barrier integrity.

● Micronutrient & amino acid assessments → ensure precursors for neurotransmitter synthesis.

● Pancreatic & digestive enzyme evaluations → optimize protein and nutrient absorption.

● Lifestyle mapping → identify stress, dietary, and sleep patterns that impact the gut.

This data enables us to create personalized protocols that restore microbial balance, support digestion, reduce inflammation, and improve mental well-being. Gut health is foundational to brain health. By addressing it, you can regain the clarity, emotional resilience, and energy to live healthily and happily.

References

● Clapp, M., et al. (2017). Gut microbiota’s effect on mental health: The gut-brain axis. Clinics and Research in Hepatology and Gastroenterology, 41(1), 18–27.

● Kelly, J. R., et al. (2016). Transferring the blues: Depression-associated gut microbiota induces neurobehavioral changes in the rat. J Neurosci, 36(36), 988–999.

● Maes, M., et al. (2008). The gut-brain barrier in major depression: LPS and cytokines. Neuro Endocrinol Lett, 29(6), 1067–1074.

● Quigley, E. M. M. (2011). Gut bacteria and the brain: Focus on psychiatric disorders. Current Opinion in Clinical Nutrition & Metabolic Care, 14(5), 476–481.