Your small intestine is protected through three major categories of defence:

1. Structural Barriers

These physical structures regulate the movement of food and bacteria through the digestive tract.

• Pyloric valve – This valve sits between the stomach and the start of the small intestine (duodenum). It controls the release of acidic, partially digested food (chyme) into the small intestine.
  
  

• Ileocecal valve – This one-way valve separates the small intestine from the large intestine. It prevents colonic bacteria from refluxing backwards into the small intestine.

If either valve becomes dysfunctional (too loose, too tight, or poorly coordinated), bacteria can move where they do not belong and contribute to SIBO.

2. Chemical Defences

Your body uses powerful chemical secretions to break down food and control bacterial populations.

• Digestive enzymes – Produced by the pancreas and present in saliva, these enzymes help break down carbohydrates, proteins, and fats. Inadequate enzyme production can lead to poor digestion and increased fermentation by bacteria.

  
  

• Hydrochloric acid (stomach acid) – Stomach acid sterilises incoming food, kills many food-borne microbes, and begins protein digestion. Low stomach acid (hypochlorhydria) is a well-known risk factor for SIBO.

  
  

• Bile – Stored in the gallbladder and released into the small intestine, bile salts emulsify fats and have natural antimicrobial properties. Poor bile flow or gallbladder dysfunction can encourage bacterial overgrowth.

3. Motility Defences

Movement is one of the most critical ways your body prevents bacterial stagnation.

• Migrating Motor Complex (MMC) – This is a housekeeping wave that sweeps through the small intestine roughly every 90 minutes during fasting. It clears leftover food particles, bacteria, and sloughed cells.

  
  

• Peristalsis – These rhythmic contractions move food through the digestive tract. If peristalsis slows (due to stress, medications, hypothyroidism, food poisoning–related nerve damage, etc.), bacteria have more time to multiply.

Although called the “small” intestine, it is the longest part of the digestive system—around 6 meters (20 feet)—so strong motility is essential to prevent stagnation.