Mental health and SIBO
Mental health and SIBO
Medically reviewed by:
Dr John Freeman
The Gut–Brain Connection
Your mental and physical health are deeply interconnected and play a vital role in your overall quality of life. One cannot truly function optimally without the other—and modern science now confirms what intuition has long suggested.
Phrases like “go with your gut,” “a gut feeling,” or “butterflies in my stomach” are more than just expressions. Research has shown that the gut functions like a “second brain,” communicating continuously with the brain through what is known as the gut–brain axis.
Stress and the Gut
Both physical and psychological stress activate the sympathetic nervous system, commonly known as the fight-or-flight response. While this response is essential for survival, it comes at a cost to digestion.
When the sympathetic nervous system is activated:
Gut motility slows
Digestive resources are redirected away from the intestines
The Migrating Motor Complex (MMC)—a crucial cleansing wave that sweeps the small intestine every 90–120 minutes—is suppressed
The MMC plays a key role in preventing bacterial buildup in the small intestine. When it is impaired, bacteria are more likely to accumulate, increasing susceptibility to small intestinal bacterial overgrowth (SIBO).
From an evolutionary perspective, this response helped humans survive immediate danger. However, in today’s world—where stress is often chronic rather than life-threatening—persistent sympathetic activation can disrupt digestion and significantly increase the risk of SIBO.
In contrast, when you are calm and relaxed after eating, the parasympathetic nervous system dominates. This is known as the rest-and-digest state, which supports:
Healthy intestinal movement
Proper digestion and absorption
Effective clearing of bacteria from the small intestine
SIBO and Brain Chemistry
What we now know...
Over the past 15 years, research into the gut–brain connection has expanded rapidly. One of the most striking discoveries is that up to 95% of the body’s serotonin is produced in the gut.
Serotonin is a neurotransmitter responsible for:
Regulating mood
Supporting emotional stability
Promoting feelings of wellbeing
Not surprisingly, studies show that individuals with IBS and SIBO experience significantly higher rates of anxiety and depression compared to the general population.
Inflammation and the Brain
SIBO is associated with increased systemic inflammation, which places the body under constant physiological stress. This inflammation:
Further disrupts gut motility
Worsens nervous system imbalance
Reinforces the stress–gut dysfunction cycle
As stress impairs digestion and impaired digestion increases stress, this becomes a self-perpetuating loop that can be difficult to break without targeted treatment.
Vitamin Deficiencies and SIBO
The small intestine—the area directly affected by SIBO—is responsible for absorbing most of the nutrients we need to maintain both physical and mental health.
Many essential nutrients cannot be produced by the body and must be obtained from food. In SIBO, bacterial overgrowth can:
Compete for nutrients
Interfere with absorption
Lead to clinically significant deficiencies
Common deficiencies seen in SIBO include iron (ferritin), vitamin D, and B vitamins, all of which play critical roles in energy production, neurological function, and mood regulation.
Iron
Iron is essential for:
Healthy red blood cell production
Oxygen transport
Energy levels
Low iron stores have been linked to fatigue, anxiety, panic attacks, low mood, and depression. Research published in Psychiatry and Clinical Neurosciences has shown that iron deficiency is associated with increased psychological distress.
Vitamin D
Vitamin D supports:
Bone health
Calcium and phosphorus absorption
Immune regulation and inflammation control
Emerging evidence also shows vitamin D plays a key role in mood regulation, with deficiencies linked to higher rates of depression.
B Vitamins
B vitamins are essential for:
Cellular energy production
Nervous system function
Brain health and neurotransmitter synthesis
Deficiencies can contribute to fatigue, brain fog, mood changes, and neurological symptoms.
A Note on Mental Health Support
If you are feeling overwhelmed, helpless, or experiencing thoughts of self-harm, please seek professional support immediately. Help is available, and you are not alone.
Suicide support hotlines:
USA: 1 (800) 273 8255
Australia: 13 11 14
Canada: 1 (833) 456 4566
New Zealand: 1737
United Kingdom: 0800 689 5652
Denmark: 45 70 20 12 01
France: 01 45 39 40 00
A full list of international crisis lines is available at: https://www.opencounseling.com/suicide-hotlines
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