What is microbiome?
The microbiome is the ecosystem of trillions of microorganisms (bacteria, fungi, viruses) living in your gastrointestinal tract. It acts as a "biological modem"—producing neurotransmitters, metabolites, and signaling molecules that influence your brain via the Vagus Nerve and bloodstream.
Key Functions
- •Neurotransmitter production — bacteria produce serotonin, GABA, and other molecules
- •SCFA production — fiber fermentation yields short-chain fatty acids that cross the Blood-Brain Barrier
- •Immune modulation — shapes systemic inflammation and neuroinflammation
- •Gut-brain axis — constant bidirectional communication with the brain
Why does the microbiome matter?
The microbiome matters because it helps digest food the body cannot break down on its own, makes certain vitamins such as vitamin K and some B vitamins, and helps train the immune system from infancy onward. A diverse, stable microbial community also crowds out harmful microbes, a protective effect known as colonization resistance.
Links between gut microbes and mood or behavior are an active research area. Animal studies show clear effects, but in humans the evidence is mostly correlational and still limited, so it is not yet clear how much the microbiome shapes mental health directly.
What affects the microbiome?
Diet is one of the strongest influences on the microbiome, especially the amount and variety of plant fiber eaten. Antibiotics can sharply reduce microbial diversity, and some communities take weeks to months to recover, while others may not fully return to their earlier state. Other factors include birth method and early feeding, age, certain medications such as proton pump inhibitors, illness, alcohol, sleep, and physical activity. Each person's microbiome is highly individual, so the same change can have different effects from one person to the next.
In ONDA Life
The Gut-Brain Axis article covers protocols for microbiome optimization: prebiotic loading, polyphenol boost, and fasting for microbial reset.