The gut microbiome: tens of trillions of residents and what they do

How many microorganisms are in the gut?

The human gut contains approximately:

3.8 × 10¹³ to 4 × 10¹³ microorganisms

amounting to about 40 trillion individuals, primarily bacteria living in the colon.

The total mass of the entire microbiota is only about 200 grams, but their gene count is hundreds of times larger than the human genome.

What does the gut microbiota do for the body?

Fiber digestion

Humans lack the enzymes to break down most types of fiber.

Gut bacteria ferment fiber and produce short-chain fatty acids (SCFAs) such as:

• Acetate
• Propionate
• Butyrate

In particular, butyrate is a vital energy source for colon cells and contributes to maintaining an anti-inflammatory environment in the gut.

Vitamin synthesis

Certain gut bacteria are capable of synthesizing:

• Vitamin K
• Biotin (B7)
• Folate (B9)
• Several other B-group vitamins

Immune system support

About 70% of the body's immune tissue is associated with the gastrointestinal tract.

The microbiota helps the immune system:

• Recognize pathogens.
• Tolerate harmless substances.
• Regulate inflammatory responses.

Protection against pathogens

Beneficial bacteria occupy space and compete for nutrients with pathogenic bacteria, helping to reduce the risk of intestinal infections.

What actually changes the microbiota?

Eating a variety of different plants

Current evidence suggests that plant food diversity is one of the most important factors in increasing microbiota diversity and promoting butyrate production.

Fermented foods

Foods such as:

• Yogurt
• Kimchi
• Pickles
• Kefir

can help increase microbiota diversity and improve certain inflammatory markers.

Antibiotics

Antibiotics can sharply reduce the number and diversity of gut bacteria.

In most cases, the microbiota will recover after a few weeks or months, but sometimes certain bacterial species may not return to their previous state.

Does the microbiota affect the brain?

Yes.

The gut and brain communicate via the Gut-Brain Axis.

Gut bacteria can:

• Produce metabolites that affect the nervous system.
• Indirectly influence serotonin production and other neural signals.
• Affect feelings of hunger, fullness, and stress levels.

However, it should be noted:

Finding a link does not mean that bacteria are the direct cause of mental illnesses or personality changes.

Many prominent results currently only show correlation and are still undergoing further research.

Why Intermittent Fasting (IF) changes the gut microbial population. Intermittent Fasting (IF) significantly alters the gut microbial population primarily by resetting circadian rhythms and creating a "starvation" phase to cleanse the digestive system. When you stop food intake for an extended period (16 hours or more), the environment within the gut changes completely, leading to the following specific impacts:

1. Synchronizing bacterial circadian rhythms Just like humans, gut bacteria have their own circadian rhythms (day and night). When eating continuously: Bacteria become disoriented; harmful bacterial species associated with obesity and inflammation thrive. When fasting: Clearly dividing eating and fasting periods helps "turn on" the bacteria's biological clock. This healthy fluctuation helps strengthen beneficial bacterial species and inhibit harmful ones.

2. Promoting the growth of "fasting-loving" bacteria When there is no external food, the species structure within the gut changes: Increase in Akkermansia muciniphila: This is a "star" bacterial species capable of consuming the mucus layer (mucin) of the intestinal lining when the body is fasting. This action stimulates the gut to produce a new, thicker mucosal layer, which strengthens the immune system, reduces inflammation, and prevents leaky gut. Increase in short-chain fatty acid (SCFA)-producing strains: Bacteria such as Bacteroidetes increase, producing beneficial fatty acids that help burn excess fat and protect the intestinal wall.

3. Activating "Cleaning Mode" (Migrating Motor Complex - MMC) When you fast for 4 hours or more after your last meal, the gut activates a wave of intense contractions called the MMC (Migrating Motor Complex). This wave acts like a broom, sweeping food debris, cellular fragments, and lingering bacteria out of the small intestine and down into the large intestine. This cleaning process prevents SIBO (Small Intestinal Bacterial Overgrowth) – a primary cause of bloating and flatulence.

4. Reducing the number of pro-inflammatory and sugar-craving bacteria Without a continuous supply of sugar and refined carbohydrates, "sweet-toothed" and opportunistic bacterial species (such as Firmicutes) are starved and decrease in number. This reduction helps you: Significantly reduce snack and sugar cravings naturally. Reduce systemic inflammatory states in the body.

Conclusion

🦠 Inside every person's body exists an ecosystem of tens of trillions of microorganisms. They not only support digestion but also participate in immunity, metabolism, and communication with the nervous system. However, this remains one of the fastest-growing fields in biomedicine, and many popular claims today still require more evidence to clearly distinguish between correlation and true causation.

Further reading

• How intermittent fasting affects the gut microbiota?
• How the immune system recognizes a virus
• What deep sleep does to your memory