SIBO Solutions: The Vicious Cycle and Under-digested Foods

By Matthew Cress, Cress Dietetics

This blog post is the written form of Matt's Youtube Video:
SIBO Solutions: The vicious cycle and under-digested foods.

A common mistake I keep seeing among people working on SIBO (Small Intestinal Bacterial Overgrowth) is that the perspective is wrong.
Many believe, “I have this bacterial overgrowth in my small intestine, so I need to kill the bacteria.”
But you don’t need to kill the bacteria.

The bacteria in your gut will naturally rebalance when you re-establish proper levels of your digestive acids and enzymes.
Let’s back up and understand why.

Understanding SIBO: What’s Really Going On

When someone has SIBO, they usually describe it like this:
“Food goes from my 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.”

They’re right that these bacteria are in the wrong place.
Most of the bacteria that support health should live in the colon (large intestine) — not in the small intestine.

The digestive tract flows as follows:
Mouth → Esophagus → Stomach → Small Intestine → Large Intestine.

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

But when the barrier between the small and large intestine becomes compromised, bacteria from the colon can backflow upward into the small intestine — where they get trapped. 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 gradient is crucial — and it’s largely controlled by pH.

The Role of pH

When food leaves the stomach, it enters the duodenum — 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.
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 — no two SIBO clients 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.

SIBO is rarely just a bacterial problem — it’s a digestion regulation problem.
The true solution is to rebuild proper digestive function, so that the system naturally keeps bacteria where they belong.

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.

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 (found in red meat, shellfish)

• Chloride (from salt)

• B Vitamins

If you’re deficient in any of these, your stomach won’t make enough acid — no matter how “acidic” your diet is.

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 — the 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,”
think:

“I need to support my digestive system so it can do its job properly.”

When you re-establish stomach acid, bile, and enzyme production, the environment itself becomes unfriendly to bacterial overgrowth.

This isn’t about fighting bacteria — it’s about creating a digestive system so efficient that overgrowth can’t happen.

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.

Once again, my name is Matthew Cress of Cress Dietetics.
Thank you for reading this primer on SIBO, and I’ll see you in the next video.

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