The human digestive tract is home to millions of microorganisms — bacteria, viruses, archaea, and even fungi. This entire ecosystem is called the gut microbiota. Its composition begins to form during fetal life and childbirth. The mode of delivery has a major influence on the early microbial profile. Infants born naturally have intestines colonized largely by lactic acid bacteria originating from the mother’s birth canal. The next stage of microbial development and reorganization depends on feeding — breastfeeding provides the greatest benefits. An infant’s gut flora is relatively unstable and shows low diversity, but as diet expands and contact with the external environment increases, new bacterial species develop, and balance gradually stabilizes.

By the age of two to three, a child’s microbiota resembles that of an adult. Each person’s microbial composition is unique, but two main bacterial phyla — Firmicutes and Bacteroidetes — dominate. The number of microorganisms changes along the digestive tract depending on oxygen availability. The fewest microbes live in the mouth and stomach, while the colon contains the most. Beyond abundance, microbial diversity and the ratio between beneficial and potentially harmful bacteria are fundamental to health.

Functions of the Gut Microbiota

Though invisible to the eye, the microbiota performs vital tasks essential for survival.

• It supports the immune system by stimulating GALT (gut-associated lymphoid tissue) cells, which is why the intestines are called the center of immunity.
• It produces bactericidal and bacteriostatic substances known as bacteriocins. Beneficial bacteria also lower pH in the large intestine, creating an acidic environment unfavorable to pathogens.
• It aids in digesting lactose. Lactobacillus and Bifidobacterium strains can break lactose down into glucose and galactose, which is why dysbiosis may cause temporary lactose intolerance.
• It ferments fiber indigestible by humans, producing short-chain fatty acids (SCFAs), an energy source for intestinal cells (colonocytes).
• It synthesizes B vitamins and vitamin K.
• It contributes to neurotransmitter production affecting mood — a fascinating link discussed further below.
• It improves the absorption of minerals and electrolytes such as sodium, magnesium, calcium, and potassium.
• It produces enzymes like hydrolases that influence lipid metabolism and cholesterol balance.

Diet and the Gut Microbiota

Diet is one of the most important factors shaping the microbiota. A diet rich in fiber from vegetables, fruits, legumes, seeds, and whole grains supports a healthy and diverse microbial community. Conversely, a diet high in processed foods, fats, sugars, and additives can disrupt microbial balance, causing dysbiosis. This imbalance is associated with digestive disorders, metabolic and autoimmune diseases, allergies, and even an increased risk of depression due to altered gut bacteria.

The Role of Short-Chain Fatty Acids (SCFAs)

SCFAs — primarily acetate, propionate, and butyrate — are produced during bacterial fermentation of fiber. Butyrate is the most studied; it provides 60–70% of colonocyte energy, stimulates mucus secretion, supports epithelial regeneration, and maintains intestinal barrier integrity. SCFAs also enter the bloodstream, influencing metabolism by improving insulin sensitivity, regulating appetite, and promoting fat breakdown. They modulate immune function and can cross the blood-brain barrier, affecting the gut-brain axis. Research links SCFAs to improvements in depression and neurodegenerative diseases such as Alzheimer’s.

The Gut-Brain Axis and Mood

The central nervous system and the digestive system communicate through the gut-brain axis. Most people know that the brain affects digestion — stress often causes stomach pain. However, newer findings show that gut microbes can influence the brain and mood in return.

This communication is bidirectional and involves neural, hormonal, and immune mechanisms. Signals from intestinal nerves reach the brain through the enteric nervous system and the vagus nerve. Biochemical communication occurs via cytokines, chemokines, neurotransmitters such as serotonin, and microbial metabolites like SCFAs. Gut bacteria produce tryptophan, the precursor to serotonin. Although intestinal serotonin cannot cross the blood-brain barrier, it affects mood indirectly by acting locally on the enteric nervous system, which is connected to the brain.