Persistent Gut Symptoms: It's Not Just What You Eat, It's How You Digest It
Inside REBUILD, the second pillar of the Gut Rewire Protocol
In the previous article in this series, I looked at RESET, the first pillar of the Gut Rewire Protocol, and how assessment and testing help us decide where to start.
But once we have that information, what happens next?
When symptoms persist, the question isn't always just what you're eating. It can also be worth looking at what your digestive system is doing with that food.
That's the focus of REBUILD, the second pillar of the Gut Rewire Protocol.
I developed the Gut Rewire Protocol by bringing together my work as a clinical naturopath and registered psychologist, with a focus on both what's happening physiologically and how changes can be made workable in everyday life.
REBUILD looks more closely at stomach function, digestive enzymes, liver and bile function, and how food moves through the digestive tract. The aim is to understand how effectively food is being broken down and nutrients made available for absorption, and which parts of that process, if any, may need support.
Digestion Is a Process, Not a Single Event
We often talk about digestion as though it's one thing. In reality, it's a sequence.
Food needs to be broken down into forms the body can absorb and use, with stomach acid, digestive enzymes and bile each playing different roles along the way. What's left then needs to move through the digestive tract.
What happens at one stage of digestion can influence what happens at the next.
That's why persistent gut symptoms like bloating, reflux, constipation, diarrhoea or symptoms after certain foods can sometimes warrant a closer look at digestion before turning our attention to the microbiome.
Stomach Function Matters
Stomach acid tends to get attention mainly because of reflux and heartburn.
But acid also has normal physiological roles in digestion. It helps begin the breakdown of food and creates the conditions needed for digestive processes further down the gastrointestinal tract.
Reflux doesn't automatically tell us what's happening with stomach acid. Health history, diet, medications and test results help determine whether stomach function is something we need to consider.
If bloating starts soon after eating, for example, that timing can be useful information and may prompt us to look more closely at what is happening earlier in digestion.
Digestive Enzymes Help Break Food Down
Digestive enzymes help break carbohydrates, proteins and fats into smaller components that can be absorbed and used by the body.
So if certain foods repeatedly cause symptoms, the question isn't always simply:
"Is this food a problem?"
It may also be worth asking whether the enzymes needed to break down that meal are doing their job effectively.
Bile, the Liver and the Gallbladder
Bile is produced by the liver and helps digest and absorb fats and fat-soluble nutrients. It also helps carry substances the body is eliminating into the digestive tract and has antimicrobial properties that can influence the intestinal environment and microbiome.
This is one reason liver function, bile production and bile delivery can form part of the REBUILD picture.
The gallbladder stores and concentrates bile before releasing it into the small intestine when we eat.
After gallbladder removal, the way bile is delivered changes. If bloating, bowel changes or difficulty tolerating fatty meals appeared afterwards, that surgical history becomes an important part of the digestive picture.
What Happens Earlier in Digestion Can Affect the Microbiome
The gut microbiome is the community of microorganisms that live in the digestive tract, with the largest and most diverse population found in the large intestine, or colon. These microbes interact with the food we eat, blie acids and other substances that reach the colon.
How well food is broken down, the amount and type of nutrients that reach the colon, bile acids, intestinal pH and how quickly food moves through the digestive tract can all help shape which microbes are better able to thrive and what they produce.
That's why jumping immediately to "fix the microbiome" can sometimes skip an important part of the picture.
Before asking only:
"Which bacteria are there?"
we also need to ask:
"What conditions are we creating for them?"
Even with something as common as bloating, REBUILD isn't about applying a standard "bloating protocol". When symptoms occur, what tends to trigger them, previous surgery, medications and how food is being digested can all help determine which part of the digestive process deserves closer attention.
What If Fibre Makes You Feel Worse?
You increase vegetables, legumes or other fibre-rich foods because they're supposed to be good for your gut, but your bloating gets worse.
That doesn't necessarily mean you "can't tolerate fibre".
It may be worth asking:
How much?
Was the amount increased significantly or quickly?
What type?
Different fibres behave differently in the digestive tract.
How well is it being digested?
How well is the food being broken down before it reaches the lower gut?
How quickly is it moving?
How quickly is food moving through the digestive tract?
What is happening in the microbiome?
How might the existing microbial environment be responding to the change?
Rather than immediately removing fibre or other foods, the fact that symptoms have worsened gives us another clue about what may need attention.
There's More to Supporting Digestion Than Supplements
Supporting digestion doesn't automatically mean trying another diet, supplement or protocol.
The first question is which part of digestion, if any, needs support. Is it stomach function, digestive enzyme activity, liver and bile function, or the way food is moving through the digestive tract?
For one person, stomach function or food breakdown may be more relevant. For another, bile flow, fat digestion or gut motility may deserve closer attention. How they eat, meal size and timing can also matter. Targeted supplementation may have a role where there is a clear reason for using it.
Digestion isn't purely mechanical either. Eating quickly between meetings is a different experience from sitting down and allowing time for a meal. Slowing down, chewing properly or taking a few calm breaths before eating can help create better conditions for digestion.
How Your Gut Responds Matters
REBUILD isn't static. How someone responds to a change can give us more information.
If bloating improves when meal size changes, symptoms shift with different amounts of fat or fibre, or bowel habits change with digestive support, those responses provide additional clues about what may be contributing.
The aim is to make each change purposeful, observe what happens, and use that information to guide what comes next, rather than moving from one diet, supplement or protocol to another.
If you've spent a long time moving from one diet, supplement or protocol to another, I explore this cycle in more detail in Stop Guessing: The Hidden Cost of Trial-and-Error Gut Health.
Next: REBALANCE
We've seen how what happens earlier in digestion can influence what reaches the colon and the conditions the gut microbiome is exposed to.
In the next article, we'll move on to REBALANCE, the third pillar of the Gut Rewire Protocol, and look more closely at the gut ecosystem: what a healthy microbiome actually means, why diversity matters, and why supporting it involves much more than simply taking a probiotic.
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