The real cause of SIBO

By Matthew Cress, Cress Dietetics

A common mistake I keep seeing among people working on SIBO (Small Intestinal Bacterial Overgrowth) is that the perspective is misguided.

"I have this bacterial overgrowth in my small intestine, so I need to kill the bacteria.”

No.

The bacterial overgrowth is a byproduct of your digestive system not producing enough stomach acid, bile, and pancreatic enzymes to digest the foods that you have during your meals. This undigested food when it sits in your gut (because you didn't digest it with stomach acid, bile and p. enzymes) gives food to SIBO bacteria and you give yourself a digestive SIBO infection.

How to treat SIBO?
Re-amplify your bodys natural digestion and the bacterial infection will naturally rebalance. The SIBO bacteria will die out (or will reduce to non-pathogenic levels), you will naturally feel better, AND you'll have better digestion.

Let’s back up and understand why.
▶️ Watch Matt's video on SIBO on his youtube channel.

Understanding SIBO: What’s Really Going On

Food goes from the mouth, through the esophagus, into the stomach, and then into the small intestine. But at that small intestine section, there are too many bacteria and they’re causing bloating, distension, pain, and indigestion.

The digestive tract flows as follows:
Mouth → Esophagus → Stomach → Small Intestine → Large Intestine.
The microbes should mainly be in the Large intestine where the microbiome is.

By the time food reaches the large intestine, only a small number of bacteria should have survived the journey. Those few then multiply and form the beneficial gut microbiome that supports digestion and overall health.

When the acids, salts, and digestive enzymes in the stomach and small intestines becomes compromised, the bacteria from the colon (large intestine) will backflow upward into the small intestine where SIBO will take hold and proliferate. That’s what causes small intestinal bacterial overgrowth.

The Three Sections of the Small Intestine

The small intestine is made up of three distinct parts:

1. Duodenum – the section right after the stomach
   

2. Jejunum – the middle section
   

3. Ileum – the final section before the large intestine
   

As you move down this pathway, the amount of bacteria should increase gradually.

• The duodenum has very few bacteria.
  

• The jejunum has a moderate amount.
  

• The ileum has more, preparing for the transition to the colon, which has the highest bacterial density.
  

This microbial gradient is crucial and it is influenced by the digestive pH.

The Role of pH

When food leaves the stomach, it enters the duodenum which is a highly acidic environment. That acidity is later neutralized by bile salts and pancreatic enzymes, which are released to help digest food.

However, if this section becomes too alkaline (not acidic enough), it creates the perfect environment for opportunistic bacteria to survive and multiply. These bacteria feed on the food that your body was not able to digest.
This often happens when stomach acid levels are too low.

When food is underdigested due to low stomach acid, it provides fuel for bacteria in the small intestine. The bacteria thrive, and this contributes directly to SIBO symptoms.

The Digestive Cascade

Here’s what I always look at when someone is dealing with SIBO:

• Is stomach acid production adequate?
  

• Is bile being properly released from the gallbladder?
  

• Are pancreatic enzymes being secreted in the right amounts?
  

Everyone is unique in this case since no two people with SIBO infections have the exact same diet, lifestyle, or digestion. That’s why a personalized approach is essential.

But generally, when the stomach isn’t acidic enough, the bile and pancreatic enzyme response downstream also becomes weak.
This creates a domino effect: poor digestion → undigested food → bacterial overgrowth → symptoms like bloating, gas, or irregular stools.

Why Killing Bacteria Doesn’t Work

You can use antimicrobial or antibiotic approaches to kill bacteria, but if you haven’t restored your body’s natural digestive defenses, the bacteria will simply return. This is the SIBO vicious cycle and the reason why people are so frustrated.

I would like to submit that SIBO is a digestion regulation problem, not just a bacterial problem. Refocusing the attention to the hosts real digestion is essential, yet rarely considered.

Reach out to Matt for an appointment if you'd like help re-amplifying your digestion and addressing your SIBO.

When stomach acid, bile, and pancreatic enzymes are present in the right amounts, bacteria from the large intestine can’t survive in the small intestine. The digestive environment itself becomes self-regulating and SIBO naturally goes away.

Building the Foundations: Nutrients for Digestion

To restore your digestion, focus on eating foods that provide the nutrients required to make your own digestive juices.

1. Stomach Acid

Your body needs specific ingredients to produce stomach acid:

• Zinc
  

• Chloride
  

• B Vitamins
  

If you’re deficient in any of these, your stomach won’t make enough stomach acid — no matter how much lemon juice and vinegar is in your diet.

When stomach acid levels are optimal, the food leaving your stomach is acidic enough to trigger bile release from the gallbladder.

2. Bile Production

Bile is made in the liver and stored in the gallbladder.
To make healthy bile, your body requires:

• Cholesterol (the liver can make it, but dietary sources help)
  

• Choline (abundant in eggs and liver)
  

• Amino acids (from protein-rich foods)
  

Interestingly, eggs are rich in both choline and cholesterol which are two key ingredients needed to make bile.
So, when you eat eggs, you’re actually providing the building blocks that help your body digest fats better.

3. Pancreatic Enzymes

Pancreatic enzymes are responsible for breaking down proteins, fats, and carbohydrates.
To produce them, your body needs:

• Amino acids (from protein)
  

• Zinc
  

• B Vitamins
  

Enzymes are proteins, so a protein-rich diet is essential.
Without enough of these nutrients, food remains partially digested, creating fuel for bacterial growth farther down the digestive tract.

Undigested Food and Stool Indicators

When food moves through the digestive system without being properly broken down, it may show up as undigested food particles in stool tests.
This is a direct sign that your body isn’t producing enough stomach acid, bile, or pancreatic enzymes.

So when someone comes to me with SIBO or digestive problems and their labs show undigested food, it makes complete sense. It’s a reflection of how the system is functioning.

The Perspective Shift

Instead of thinking, “I need to kill the bacteria causing SIBO,”

Reframe it with: “I need to support my digestive system so it can digest the food I eat and doesn't leave the door open for digestive infections.”

Final Thoughts

These are the perspective shifts I try to bring to every conversation about digestion and gut health.
When you aim to restore function instead of destroy bacteria, you empower your body to heal naturally.

If you have questions about how I apply this methodology with clients, let me know in the comments below. If you'd like to work with Matt either reach out or book an appointment.

Associated Youtube video: SIBO Solutions: The vicious cycle and under-digested foods.